Morris was born on February 5, 1948, and raised in a Jewish family in Hewlett, New York.

After finishing Vernon, Florida, Morris tried to get funding for a variety of projects. There was Road, a story about an interstate highway in Minnesota; a project about Robert Golka, the creator of laser-induced fireballs in Utah; and the story of Centralia, Pennsylvania, the coal town in which an inextinguishable subterranean fire ignited in 1962. He eventually got funding in 1983 to write a script about John and Jim Pardue, a pair of Missouri bank Robbers who had killed their father and grandmother and robbed five banks. Morris's pitch went, "The great bank-robbery sprees always take place at a time when something is going wrong in the country. Bonnie and Clyde were apolitical, but it's impossible to imagine them without the Depression as a back-drop. The Pardue brothers were apolitical, but it's impossible to imagine them without Vietnam." Morris wanted Tom Waits and Mickey Rourke to play the brothers, and he wrote the script, but the project eventually failed. Morris worked on writing scripts for various other projects, including a pair of ill-fated Stephen King adaptations.

In 2012, Morris published his second book, A Wilderness of Error: The Trials of Jeffrey MacDonald, about Jeffrey MacDonald, the Green Beret physician convicted of killing his wife and two daughters on February 17, 1970. Morris first became interested in the case in the early 1990s and believes that MacDonald is not guilty after undertaking extensive research. Morris explained in a July 2013 interview, prior to the reopening of the case: "What happened here is wrong. It's wrong to convict a man under these circumstances. And if I can help correct that, I will be a happy camper."

Morris left Princeton in 1972, enrolling at Berkeley as a Ph.D. student in philosophy. At Berkeley, he once again found that he was not well-suited to his subject. "Berkeley was just a world of pedants. It was truly shocking. I spent two or three years in the philosophy program. I have very bad feelings about it," he later said. He became a regular at the Pacific Film Archive. As Tom Luddy, the Director of the archive at the time, later remembered: "He was a film noir nut. He claimed we weren't showing the real film noir. So I challenged him to write the program notes. Then, there was his habit of sneaking into the films and denying that he was sneaking in. I told him if he was sneaking in he should at least admit he was doing it."

Inspired by Hitchcock's Psycho, Morris visited Plainfield, Wisconsin in 1975. While in Wisconsin, he conducted multiple interviews with Ed Gein, the infamous serial killer who resided at Mendota State Hospital in Madison. He later made plans with German film Director Werner Herzog, whom Tom Luddy had introduced to Morris, to return in the summer of 1975 to secretly open the grave of Gein's mother to test their theory that Gein himself had already dug her up. Herzog arrived on schedule, but Morris had second thoughts and was not there. Herzog did not open the grave. Morris later returned to Plainfield, this time staying for almost a year, conducting hundreds of hours of interviews. Although he had plans to either write a book or make a film (which he would call Digging up the Past), Morris never completed his Ed Gein project.

Adams was serving a life sentence that had been commuted from a death sentence on a legal technicality for the 1976 murder of Robert Wood, a Dallas police officer. Adams told Morris that he had been framed, and that David Harris, who was present at the time of the murder and was the principal witness for the prosecution, had in fact killed Wood. Morris began researching the case because it related to Dr. Grigson. He was at first unconvinced of Adams's innocence. After reading the transcripts of the trial and meeting David Harris at a bar, however, Morris was no longer so sure.

After spending two weeks in Vernon, Morris returned to Berkeley and began working on a script for a work of fiction that he called Nub City. After a few unproductive months, he happened to read a headline in the San Francisco Chronicle that read, "450 Dead Pets Going To Napa Valley". Morris left for Napa Valley and began working on the film that would become his first feature, Gates of Heaven. In 1978, when the film premiered, Werner Herzog cooked and publicly ate his shoe, an event later incorporated into a short documentary by Les Blank. Herzog had promised to eat his shoe if Morris completed the project, to challenge and encourage Morris, whom Herzog perceived as incapable of following up on the projects he conceived. At the public shoe-eating, Herzog suggested that he hoped the act would serve to encourage anyone having difficulty bringing a project to fruition.

Gates of Heaven was given a limited release in the spring of 1981. Critic Roger Ebert was and remained a champion of the film, including it on his all-time top ten best films list. Morris returned to Vernon in 1979 and again in 1980, renting a house in town and conducting interviews with the town's citizens. Vernon, Florida premiered at the 1981 New York Film Festival. Newsweek called it, "a film as odd and mysterious as its subjects, and quite unforgettable." The film, like Gates of Heaven, suffered from poor distribution. It was released on video in 1987, and DVD in 2005.

In 1984, Morris married Julia Sheehan, whom he had met in Wisconsin while researching Ed Gein and other serial killers. He would later recall an early conversation with Julia: "I was talking to a mass murderer but I was thinking of you," he said, and instantly regretted it, afraid that it might not have sounded as affectionate as he had wished. But Julia was actually flattered: "I thought, really, that was one of the nicest things anyone ever said to me. It was hard to go out with other guys after that."

In 1985, Morris became interested in Dr. James Grigson, a Psychiatrist in Dallas. Under Texas law, the death penalty can only be issued if the jury is convinced that the defendant is not only guilty, but will commit further violent crimes in the Future if he is not put to death. Grigson had spent 15 years testifying for such cases, and he almost invariably gave the same damning testimony, often saying that it is "one hundred per cent certain" that the defendant would kill again. This led to Grigson being nicknamed "Dr. Death". Through Grigson, Morris would meet the subject of his next film, 36-year-old Randall Dale Adams.

At the time, Morris had been making a living as a private investigator for a well-known private detective agency that specialized in Wall Street cases. Bringing together his talents as an investigator and his obsessions with murder, narration, and epistemology, Morris went to work on the case in earnest. Unedited interviews in which the prosecution's witnesses systematically contradicted themselves were used as testimony in Adams's 1986 habeas corpus hearing to determine if he would receive a new trial. David Harris famously confessed, in a roundabout manner, to killing Wood.

The Thin Blue Line ranks among the most critically acclaimed documentaries ever made. According to a survey by The Washington Post, the film made dozens of critics' top ten lists for 1988, more than any other film that year. It won the documentary of the year award from both the New York Film Critics Circle and the National Society of Film Critics. Despite its widespread acclaim, it was not nominated for an Oscar, which created a small scandal regarding the nomination practices of the Academy. The Academy cited the film's genre of "non-fiction", arguing that it was not actually a documentary.

In 2002, Morris was commissioned to make a short film for the 75th Academy Awards. He was hired based on his advertising resume, not his career as a Director of feature-length documentaries. Those interviewed ranged from Laura Bush to Iggy Pop to Kenneth Arrow to Morris's 15-year-old son Hamilton. Morris was nominated for an Emmy for this short film. He considered editing this footage into a feature-length film, focusing on Donald Trump discussing Citizen Kane (this segment was later released on the second issue of Wholphin). Morris went on to make a second short for the 79th Academy Awards in 2007, this time interviewing the various nominees and asking them about their Oscar experiences.

In 2003, Morris won the Oscar for Best Documentary for The Fog of War, a film about the career of Robert S. McNamara, the Secretary of Defense during the Vietnam War under Presidents John F. Kennedy and Lyndon B. Johnson. In the haunting opening about McNamara’s relationship with U.S. General Curtis LeMay during World War II, Morris brings out complexities in the character of McNamara, which shaped McNamara's positions in the Cuban missile crisis and the Vietnam War. Like his earlier documentary, The Thin Blue Line, The Fog of War included extensive use of re-enactments, a technique which many had believed was inappropriate for documentaries.

In late 2004, Morris directed a series of noteworthy commercials for Sharp Electronics. The commercials enigmatically depicted various scenes from what appeared to be a short narrative that climaxed with a car crashing into a swimming pool. Each commercial showed a slightly different perspective on the events, and each ended with a cryptic weblink. The weblink was to a fake webpage advertising a prize offered to anyone who could discover the secret location of some valuable urns. It was in fact an alternate reality game. The original commercials can be found on Morris's website.

Morris directed a series of commercials for Reebok that featured six prominent National Football League (NFL) players. The 30-second promotional videos were aired during the 2006 NFL season.

In early 2010, a new Morris documentary was submitted to several film festivals, including Toronto International Film Festival, Cannes Film Festival, and Telluride Film Festival. The film, titled Tabloid, features interviews with Joyce McKinney, a former Miss Wyoming, who was convicted in absentia for the kidnap and indecent assault of a Mormon missionary in England during 1977.

Morris has also written long-form journalism, exploring different areas of interest and published on The New York Times website. A collection of these essays, titled Believing is Seeing: Observations on the Mysteries of Photography, was published by Penguin Press on September 1, 2011. In November 2011, Morris premiered a documentary short titled "The Umbrella Man"—featuring Josiah "Tink" Thompson—about the Kennedy assassination on The New York Times website.

In 2013, Morris stated that he has made around 1,000 commercials during his career.

In the 10th grade, Morris attended The Putney School, a boarding school in Vermont. He began playing the cello, spending a summer in France studying music under the acclaimed Nadia Boulanger, who also taught Morris's Future collaborator Philip Glass. Describing Morris as a teenager, Mark Singer wrote that he "read with a passion the fourteen-odd Oz books, watched a lot of television, and on a regular basis went with a doting but not quite right maiden aunt ('I guess you'd have to say that Aunt Roz was somewhat demented') to Saturday matinées, where he saw such films as This Island Earth and Creature from the Black Lagoon — horror movies that, viewed again 30 years later, still seem scary to him."