Charles Manson's biological father appears to have been Colonel Walker Henderson Scott Sr. (1910–1954) against whom Kathleen Maddox filed a paternity suit that resulted in an agreed judgment in 1937. Manson might have never known his biological father. Scott worked intermittently in local mills, and also had a local reputation as a con Artist. He allowed Maddox to believe that he was an army colonel, although "Colonel" was merely his given name. When Maddox told him she was pregnant, he told her that he had been called away on army business; after several months she realised he had no intention of returning.

Manson was born to unmarried 16-year-old Kathleen Manson-Bower-Cavender, née Maddox (1918–1973), in the General Hospital, in Cincinnati, Ohio. Manson was first named "no name Maddox". Within weeks, he was called Charles Milles Maddox.

In August 1934, before Manson's birth, Maddox married william Eugene Manson (1909–1961), whose occupation was listed on Charles' birth certificate as a "laborer" at a dry cleaning Business. Maddox went on drinking sprees for days at a time with her brother, Luther, leaving Charles with a variety of babysitters. They were divorced on April 30, 1937, when a court accepted Manson's charge of "gross neglect of duty".

On August 1, 1939, Maddox and Luther's girlfriend, Julia Vickers, spent the evening drinking with a new acquaintance, Frank Martin, who appeared to be wealthy. Maddox and Vickers decided to rob him, and Maddox phoned her brother to help. They were incompetent thieves, and were found and arrested within hours. At the trial seven weeks later, Luther was sentenced to ten years, and Kathleen was sentenced to five years. Manson was placed in the home of an aunt and uncle in McMechen, West Virginia. His mother was paroled in 1942. Manson later characterized the first weeks after she returned from prison as the happiest time in his life.

They moved to Charleston where Manson continually played truant, and his mother spent her evenings drinking. She was arrested for grand larceny, but not convicted. After moving to Indianapolis, Maddox started attending Alcoholics Anonymous meetings, where she met an alcoholic named Lewis (no first name), whom she married in August 1943. As well as constantly playing truant, Manson began stealing from stores and from his home. In 1947, Maddox looked for a temporary foster home for Manson, but she was unable to find a suitable one. She decided to send him to the Gibault School for Boys in Terre Haute, Indiana, a school for male delinquents run by Catholic Priests. He soon fled home to his mother, but she took him back to the school. He spent Christmas 1947 in McMechen, at the house of his aunt and uncle, where he was caught stealing a gun.

On a psychiatrist's recommendation, Manson was transferred in October 1951 to Natural Bridge Honor Camp, a minimum security institution. His aunt visited him and told administrators she would let him stay at her house and would help him find work. He had a parole hearing scheduled for February 1952. However, in January, he was caught raping a boy at knifepoint. He was transferred to the Federal Reformatory in Petersburg, Virginia, where he committed a further "eight serious disciplinary offenses, three involving homosexual acts", and then to a maximum security reformatory at Chillicothe, Ohio, where he was expected to stay until his release on his 21st birthday in November 1955. Good behavior led to an early release in May 1954, to live with his aunt and uncle in McMechen.

In January 1955, he married a hospital waitress named Rosalie Jean Willis. Around October, about three months after he and his pregnant wife arrived in Los Angeles in a car he had stolen in Ohio, Manson was again charged with a federal crime, for taking the vehicle across state lines. After a psychiatric evaluation, he was given five years' probation. His subsequent failure to appear at a Los Angeles hearing on an identical charge filed in Florida resulted in his March 1956 arrest in Indianapolis. His probation was revoked; he was sentenced to three years' imprisonment at Terminal Island, San Pedro, California.

While Manson was in prison, Rosalie gave birth to their son Charles Manson Jr. During his first year at Terminal Island, Manson received visits from Rosalie and his mother, who were now living together in Los Angeles. In March 1957, when the visits from his wife ceased, his mother informed him Rosalie was living with another man. Less than two weeks before a scheduled parole hearing, Manson tried to escape by stealing a car. He was subsequently given five years probation, and his parole was denied.

Manson received five years' parole in September 1958, the same year in which Rosalie received a decree of divorce. By November, he was pimping a 16-year-old girl and was receiving additional support from a girl with wealthy parents. In September 1959, he pleaded guilty to a charge of attempting to cash a forged U.S. Treasury check, which he claimed to have stolen from a mailbox; the latter charge was later dropped. He received a 10-year suspended sentence and probation after a young woman with an arrest record for prostitution made a "tearful plea" before the court that she and Manson were "deeply in love ... and would marry if Charlie were freed". Before the year's end, the woman did marry Manson, possibly so testimony against him would not be required of her.

The woman's name was Leona. As a prostitute, she had used the name Candy Stevens. After Manson took her and another woman from California to New Mexico for purposes of prostitution, he was held and questioned for violation of the Mann Act. Though he was released, he correctly suspected that the investigation had not ended. When he disappeared in violation of his probation, a bench warrant was issued. An indictment for violation of the Mann Act followed in April 1960. When one of the women was arrested for prostitution, Manson was arrested in June in Laredo, Texas and was returned to Los Angeles. For violation of his probation on the check-cashing charge, he was ordered to serve his 10-year sentence.

Although the Mann Act charge had been dropped, the attempt to cash the Treasury check was still a federal offense. His September 1961 annual review noted he had a "tremendous drive to call attention to himself", an observation echoed in September 1964. In 1963, Leona was granted a divorce, in the pursuit of which she alleged that she and Manson had a son, Charles Luther.

According to a popular urban legend, Manson unsuccessfully auditioned for the Monkees in late 1965; this is refuted by the fact that Manson was still incarcerated at McNeil Island at that time.

In June 1966, Manson was sent for the second time to Terminal Island in preparation for early release. By the time of his release day on March 21, 1967, he had spent more than half of his 32 years in prisons and other institutions. This was mainly because he had broken federal laws. Federal sentences were, and remain, much more severe than state sentences for many of the same offenses. Telling the authorities that prison had become his home, he requested permission to stay, a fact mentioned in a 1981 television interview with Tom Snyder.

In 2009, a Los Angeles DJ and Songwriter named Matthew Roberts released correspondence and other evidence indicating that he may have been biologically fathered by Manson. Roberts' biological mother claims to have been a member of the Manson Family who left in mid-1967 after being raped by Manson; she returned to her parents' home to complete the pregnancy, gave birth on March 22, 1968, and subsequently put Roberts up for adoption. Manson himself stated that he "could" be the father, acknowledging the biological mother and a sexual relationship with her during 1967; this was nearly two years before the Family began its murderous phase.

In the late 1960s, Manson attracted a quasi-communal cult based in California that was later dubbed the "Manson Family". The group was involved in the murder of Gary Hinman in July 1969, then gained national notoriety after the murder of Actress Sharon Tate and four others in her home on August 9, 1969, and Leno and Rosemary LaBianca the next day. The Tate–LaBianca Murders were executed by Tex Watson and three other members of the Family, acting under the specific instructions of Manson. Family members were also responsible for other assaults, thefts, crimes, and the attempted assassination of United States President Gerald Ford in Sacramento.

Beginning in January 1970, Manson was embraced by the underground newspapers Los Angeles Free Press and Tuesday's Child, with the latter proclaiming him "Man of the Year". In June 1970, he was the subject of a Rolling Stone cover story, "Charles Manson: The Incredible Story of the Most Dangerous Man Alive". When a Rolling Stone Writer visited the Los Angeles District Attorney's office in preparing that story, he was shocked by a photograph of the bloody "Healter [sic] Skelter" that would bind Manson to popular culture. Bugliosi pointed out the dispute in the underground press over whether Manson was "Christ returned" or "a sick symbol of our times" to his Helter Skelter co-author, Curt Gentry. Bernardine Dohrn, a leader of the Weather Underground, reportedly said of the Tate murders: "Dig it, first they killed those pigs, then they ate dinner in the same room with them, then they even shoved a fork into a victim's stomach. Wild!"

On December 13, 1971, Manson was convicted of first-degree murder in Los Angeles County Court for the July 25, 1969, death of musician Gary Hinman. He was also convicted of first-degree murder for the August 1969 death of Donald Jerome "Shorty" Shea. A footnote to the conclusion of California v. Anderson, the 1972 decision that neutralized California's death sentences, stated that, "any prisoner now under a sentence of death … may file a petition for writ of habeas corpus in the superior court inviting that court to modify its judgment to provide for the appropriate alternative punishment of life imprisonment or life imprisonment without possibility of parole specified by statute for the crime for which he was sentenced to death." This made Manson eligible to apply for parole after seven years' incarceration. Accordingly, his first parole hearing took place on November 16, 1978, at California Medical Facility in Vacaville, and his petition was rejected.

In the 1980s, Manson gave four interviews. The first, recorded at California Medical Facility and aired June 13, 1981, was by Tom Snyder for NBC's The Tomorrow Show. The second, recorded at San Quentin State Prison and aired March 7, 1986, was by Charlie Rose for CBS News Nightwatch; it won the national news Emmy Award for "Best Interview" in 1987. The third, with Geraldo Rivera in 1988, was part of that journalist's prime-time special on Satanism. At least as early as the Snyder interview, Manson's forehead bore a swastika, in the spot where the X carved during his trial had been.

On September 25, 1984, Manson was imprisoned in the California Medical Facility at Vacaville when a fellow inmate, Jan Holmstrom, poured paint thinner on him and set him on fire, causing second- and third-degree burns on over 20 percent of his body. Holmstrom explained that Manson had objected to his Hare Krishna chants and verbally threatened him.

In 1989, Nikolas Schreck conducted an interview with Manson, cutting the interview up for material in his documentary Charles Manson Superstar. Schreck concluded that Manson was not insane, but merely acting that way out of frustration.

The first song to deal with Manson and his followers was probably Revolution Blues, a short song on Neil Young's On the Beach album. In bizarre images, it depicts the world view from the perspective of the 'Family' members. American rock band Guns N' Roses recorded Manson's "Look at Your Game, Girl", included as an unlisted 13th track on their 1993 album "The Spaghetti Incident?" "My Monkey", which appears on Portrait of an American Family by the American rock band Marilyn Manson, includes the lyrics "I had a little monkey / I sent him to the country and I fed him on gingerbread / Along came a choo-choo / Knocked my monkey cuckoo / And now my monkey's dead." These lyrics are from Manson's "Mechanical Man", which is heard on LIE. Crispin Glover covered "Never Say 'Never' To Always" on his album The Big Problem ≠ The Solution. The Solution = Let It Be released in 1989.

In an afterword composed for the 1994 edition of the non-fiction book Helter Skelter, prosecutor Vincent Bugliosi quoted a BBC employee's assertion that a "neo-Manson cult" existing then in Europe was represented by, among other things, approximately 70 rock bands playing songs by Manson and "songs in support of him".

In June 1997, a prison disciplinary committee found that Manson had been trafficking drugs. That August, he was moved from Corcoran State Prison to Pelican Bay State Prison.

Three people have stated their intention to claim Manson's estate and body. Manson's grandson, Jason Freeman, stated his intent to take possession of Manson's remains and personal effects. Michael Channels, a pen pal of Manson has a will, dated February 14, 2002, that leaves Manson's entire estate plus Manson's body to Channels. A friend of Manson's, Ben Gurecki, has a will dated January 2017, that gives the estate and Manson's body to Manson's alleged son, Matthew Roberts. In 2012, CNN News ran a DNA match to see if Freeman and Roberts were related to each other and found that they were not. (Matches between Roberts and Manson were attempted but the results were reportedly "contaminated".) On March 12, 2018, the Kern County Superior Court in California decided in favor of Freeman in regard to the body of Manson, which Freeman had previously said he would have cremated.

On September 5, 2007, MSNBC aired The Mind of Manson, a complete version of a 1987 interview at California's San Quentin State Prison. The footage of the "unshackled, unapologetic, and unruly" Manson had been considered "so unbelievable" that only seven minutes of it had originally been broadcast on The Today Show, for which it had been recorded.

In March 2009, a photograph taken of Manson, showing a receding hairline, grizzled gray beard and hair and the swastika tattoo still prominent on his forehead, was released to the public by California corrections officials.

In 2010, Manson recorded an album of acoustic pop songs with additional production by Henry Rollins, titled Completion. Only five copies were pressed; two belong to Rollins, while the other three are presumed to have been with Manson. The album remains unreleased.

On April 11, 2012, Manson was denied release at his 12th parole hearing, which he did not attend. Since his March 27, 1997 parole hearing, Manson refused to attend any of his Future hearings. The panel at that hearing noted that Manson had a "history of controlling behavior" and "mental health issues" including schizophrenia and paranoid delusional disorder, and was too great a danger to be released. The panel also noted that Manson had received 108 rules violation reports, had no indication of remorse, no insight into the causative factors of the crimes, lacked understanding of the magnitude of the crimes, had an exceptional, callous disregard for human suffering and had no parole plans. It was determined that Manson would not be reconsidered for parole for another 15 years (i.e. not before 2027, at which time he would have been 92 years old).

Since that time, there have been several releases of Manson recordings – both musical and spoken. One of these, The Family Jams, includes two compact discs of Manson's songs recorded by the Family in 1970, after Manson and the others had been arrested. Guitar and lead vocals are supplied by Steve Grogan; additional vocals are supplied by Lynette Fromme, Sandra Good, Catherine Share, and others. One Mind, an album of music, poetry, and spoken word, new at the time of its release, in April 2005, was put out under a Creative Commons license.

In 2014, it was announced that Manson was engaged to 26-year-old Afton Elaine "Star" Burton while he was still in prison, and it was also announced that he had obtained a marriage license on November 7. Burton had been visiting Manson in prison for at least nine years, and she maintained several websites that proclaimed his innocence. The wedding license expired on February 5, 2015, without a marriage ceremony taking place. It was later reported that, according to Journalist Daniel Simone, the wedding was cancelled after it was discovered that Burton only wanted to marry Manson so she and a friend, Craig "Gray Wolf" Hammond, could use his corpse as a tourist attraction after his death. According to Simone, Manson believed he would never die, and may just have been using the possibility of marriage as a way to encourage Burton and Hammond to continue visiting him and bringing him gifts. Together with a co-author Heidi Jordan Ley and with the assistance of some of Manson's fellow prisoners, Simone wrote a book about Manson and was seeking a publisher for it. Burton said on her web site that the reason the marriage did not take place is merely logistical – that Manson was suffering from an infection and had been in a prison medical facility for two months, and could not receive visitors. She said she still hoped the marriage license would be renewed and the marriage would take place.

On November 15, 2017, a source not authorized to speak on behalf of the corrections department confirmed that Manson had returned to a hospital in Bakersfield. In compliance with federal and state medical privacy laws, the California Department of Corrections and Rehabilitation did not confirm this. He died from cardiac arrest resulting from respiratory failure and colon cancer at the hospital four days later on November 19.

Quentin Tarantino has announced that his newest project will be about Manson, titled "Once Upon a Time in Hollywood", set to release in 2019.