Madhavan B. Nair was born and raised in Neyyattinkara, a major industrial and commercial area located south of Trivandrum, the capital city of Kerala. He is from the Thalakulam Kunnakode family and is the son of Rajyasree Bhaskara Pillai and Rugmini Amma. Madhavan is the fourth of six siblings.

His father, Rajyasree Bhaskara Pillai, was a freedom fighter and the editor and owner of Rajyasree Newspaper. He was a contemporary of Swadeshabhimani Ramakrishna Pillai, a social reformer and a native of Neyyattinkara.

Madhavan currently resides in Chatham, New Jersey, with his wife Geetha Nair, originally from Kazhakuttam, Trivandrum. They have two children, Bhaskar M. Nair and Janaki Nair. Bhaskar is married to Anamika Nair, and they have two children, Rohan and Anaya Nair. Janaki, who was married to Mahesh Avula and had a daughter, Nishika Avula, passed away in 2019 due to cancer. In her memory, MBN founded the MBN Foundation, which focuses on promoting skills and preventing cancer.