Choudhary, 62, was admitted at a private South Delhi hospital after his condition deteriorated last evening.
He passed away at around 8 PM today, family sources said. He is survived by his wife and two sons.
His body will be taken to Bardhaman, his native place, from Kolkatta for the last rites.
A five-time MP, Choudhary, formed his party, the Party of Democratic Socialism (PDS), following his differences with the CPIM leadership.
He was also the President of the Students Federation of India when he was first elected as an MP from Katwa parliamentary constituency in 1980 in West Bengal.