M. S. Swaminathan was born in Kumbakonam on 7 August 1925. He was the second son of surgeon Dr. M.K. Sambasivan and Parvati Thangammal Sambasivan. M.S. Swaminathan learnt from his Father, "that the word 'impossible' exists mainly in our minds and that given the requisite will and effort, great tasks can be accomplished." Surgeon M.K. Sambasivam, a follower of Mahatma Gandhi, took the lead in Kumbakonam in "burning his foreign clothes," a symbolic act in support of the Swadeshi movement: which emphasized the use of Indian rather than foreign-made clothes, and handloomed rather than mill-spun cloth. The political purpose of the swadeshi movement was to free India from dependence on foreign imports and to protect village industry. His Father led in opening the temples to [Dalit]s, part of the temple entry movement of the Indian independence movement in Tamil Nadu, and in eradicating filariasis in Kumbakonom, an area long infected with the dread disease. The sense of Service to one's fellow man was thus ingrained in him early.

Swaminathan then decided to pursue a career in agricultural sciences. He enrolled in Madras Agricultural College ( now the Tamil Nadu Agricultural University ) where he graduated as valedictorian with another Bachelor of Science degree, this time in Agricultural Science. He explained this career decision thus: "My personal motivation started with the great [Bengal famine of 1943], when I was a student at the University of Kerala. There was an acute rice shortage, and in Bengal about 3 million people died from starvation. All of our young people, myself included, were involved in the freedom struggle, which Gandhi had intensified, and I decided I should take to agricultural research in order to help farmers produce more."

In 1947, the year of Indian independence he moved to the Indian Agricultural Research Institute (IARI) in New Delhi as a post-graduate student in genetics and plant breeding. He obtained a post-graduate degree with high distinction in Cytogenetics in 1949. He wrote the Union Public Service Commission exam and qualified for the Indian Police Service.

Dr Swaminathan is a prolific scientific researcher and Writer. He published 46 single-author papers between 1950 and 1980. Out of 118 two author papers, he was first author of 80. Out of 63 three-author papers he was first author of 15. Out of 21 four-author papers he was first author of 9. In total he had 254 papers to his credit, 155 of which he was the single or first author. His scientific papers are in the fields of crop improvement (95), cytogenetics and genetics (87) and phylogenetics (72). His most frequent publishers were Indian Journal of Genetics (46), Current Science (36), Nature (12) and Radiation Botany (12). Some of the papers are listed below.

M.S. Swaminathan is married to Mina Swaminathan, whom he met in 1951 while they were both studying at Cambridge. They live in Chennai, Tamil Nadu. They have three daughters and five grandchildren. Their daughters are Dr. Soumya Swaminathan, the Deputy Director General of World Health Organization, Dr. Madhura Swaminathan, who is a Professor of Economics at the Indian Statistical Institute, Bangalore and Nitya Swaminathan, a Senior Lecturer in Gender Analysis and Development at the University of East Anglia.

Swaminathan then accepted a post-doctoral research associateship at the University of Wisconsin, Department of Genetics to help set up a USDA potato research station. Despite his strong personal and professional satisfaction with the research work in Wisconsin, he declined the offer of a full-time faculty position, returning to India in early 1954.

From 1972 to 1979 he was Director general of the Indian Council of Agricultural Research. He was Principal Secretary, Ministry of Agriculture from 1979 to 1980. He served as Director General of the International Rice Research Institute (1982–88) and became President of the International Union for the Conservation of Nature and Natural Resources in 1988.

Despite these awards and honours, the credibility of Swaminathan and his promotion of biotechnology remains open to question by some. His record retains some controversy. In 1967 Swaminathan published a paper on a variety called Sharbati Sonora which he claimed had more lysine than the Mexican strains from which it was derived. It was re-examined by CIMMYT and found in 1969 to be incorrect. In 1972 Vinod Shah, an agronomist at the ICAR committed suicide and claimed that Swaminathan collected poor quality data to support his ideas. A committee was set up and an investigation was conducted into the Sharbati Sonora case. It was determined that someone had intentionally altered the value of the lysine content so that Sharbati Sonora was viewed positively. The report of the committee noted that it was not an isolated incident and that such practice "pervades the entire scientific and academic community in this country. At the root of it is the greed for bureacratic power and love of a comfortable life that afflicts this class." The first among those who came to expose many of the claims made by MS Swaminathan was Claude Alvares. In his article The Great Gene Robbery 23 March 1986 The Illustrated Weekly. Alvares provided arguments to show that most of the research that was initiated by him and the International Rice Research Institute was not original. Shiv Vishwanathan in an EPW article wrote he is a sociological phenomenon. He is paradigm, exemplar, dissenter, critic and alternative. .....Swaminathan always assimilates the new. Claude Alvares gives a different picture:

On the occasion of the presentation of the First World Food Prize to Swaminathan in October 1987, Javier Perez de Cuellar, Secretary General of the United Nations, wrote: "Dr. Swaminathan is a living legend. His contributions to Agricultural Science have made an indelible mark on food production in India and elsewhere in the developing world. By any standards, he will go into the annals of history as a world scientist of rare distinction."

He was one of three from India included in Time magazine's 1999 list of the "20 most influential Asian people of the 20th century," the other two being Mahatma Gandhi and Rabindranath Tagore.

Swaminathan was the featured speaker at the 2006 Norman E. Borlaug International Symposium in Des Moines, Iowa on, 19 October 2006. He was sponsored by Humanities Iowa, an affiliate of the National Endowment for the Humanities. Swaminathan presented the "Third Annual Governor's Lecture" and spoke on "THE GREEN REVOLUTION REDUX: Can we replicate the single greatest period of food production in all human history?" about the cultural and social foundations of the Green Revolution in India and the role of historic Leaders in India, such as Mahatma Gandhi, in inspiring the Green Revolution there by calling for the alleviation of widespread hunger. He talked about the links between Gandhi and the great Iowa scientist George Washington Carver.