Subramaniam was born to V. Lakshminarayana Iyer and Seethalakshmi, both accomplished musicians.

He lived in Jaffna during his younger years, taking up music studies before the age of five. He began training in violin under the tutelage of his father, Professor V. Lakshminarayana. "Mani", as he is fondly known by fellow musicians and his family, gave his first public performance at the age of six.

His uncles include Ramnad Raghavan and Ramnad Krishnan. His brothers are also acclaimed musicians, and include the violinist-composers L. Shankar (alias. Shenkar), and the late L. Vaidyanathan. He has released recordings with both.

Subramaniam developed a passion for music as well as science from a young age, studying Medicine and acquiring his M.B.B.S. at Madras Medical College. He registered as a General Practitioner, before deciding to pursue music full-time. He has a Master's degree in Western classical music, which he acquired at the California Institute of the Arts.
Subramaniam was married to Viji (Vijayashree Shankar) Subramaniam, who died on 9 February 1995 and since November 1999 has been married to theIndian playback singer Kavita Krishnamurthy. He has four children with Viji  Narayana Subramaniam, Gingger Shankar, Bindu Subramaniam, and Ambi Subramaniam.

He continues to perform pieces with his daughter singer/songwriter Bindu Subramaniam, violin duets with his son, Ambi Subramaniam, and has further recorded and given several concerts with Krishnamurthy. Their collaborations have earned them the nickname Subramaniam Gharana. He also performs with his eldest son Dr. Narayana Subramaniam.