Lamenting over the decision, he said that support to Pranab was a 'grave error'.
"I protest against the decision by the Polit Bureau to support the candidature of Pranab Mukherjee. I consider this to be a grave error which will harm the party and disturb Left unity," Bose said in a statement.
There was, however, no comment from the CPM on Bose's resignation.
"The same leadership is committing yet another costly mistake, refusing to learn anything from the past. Party members are aghast and exasperated that their concerns are falling on deaf ears. Therefore, with great pain and agony, I tender my resignation from the primary membership of the Party," said Bose.
Bose also attacked CPM General Secretary Prakash Karat and said that his comments were "wholly misleading".
"In the absence of any explicit and coherent explanation so far, one can only make two guesses. If the consideration was that the strength of CPI (M) and the Left is numerically too weak to field its own candidate against both Congress and BJP-backed candidates, then the natural choice should have been to abstain from the polls."
"That is the stand adopted by CPI and the RSP and it is an eminently reasonable, transparent and principled position," he said.
The left is divided over choosing the Presidential candidate. While the CPM said it will back Pranab Mukherjee, the RSP and CPI said that would not vote.