Swaminathan was born in Kumbakonam, Thanjavur district (Madras Presidency) on August 7, 1925, to M K Sambasivan and Parvati Thangammal. M K Sambasivan was a general surgeon, and he passed away when Swaminathan was 11 years old. After his father’s death, Swaminathan was looked after by his paternal uncle.

Swaminathan was educated at a local high school and later at the Catholic Little Flower High School in Kumbakonam. Even as a child, he enjoyed spending time in the farm lands and with the farmers. He witnessed the impact fluctuations in crop prices had on his family, and the damage erratic weather caused on crops as well as the hardship farmers had to face because of poor incomes.

His family preferred that he take up medicine and be a doctor like his father, but Swaminathan took up Zoology at Travancore University in 1944. The shortage of food during World War II and the Bengal famine of 1943, had a tremendous influence on Swaminathan. He turned to agriculture, and earned his second B Sc from Coimbatore Agricultural College, Madras University in 1947.

He married Mina Boothalingam, whom he met in 1951 while they were both studying at Cambridge. They have three daughters – Soumya Swaminathan, Madhura Swaminathan and Nitya Rao.