Shashank Manohar had earlier criticized the boards decision retain Raman post the 2013 IPL spot-fixing scandal.
The controversial cricket administrators resignation was accept by the Board of Control for Cricket in India (BCCI) and he is expected to end his association with the Indian board on November 5.
According to ESPNCricinfo, Raman was told by Manohar to resign voluntarily or face the sack during BCCIs annual general meeting on November 9.
Raman submitted his resignation on Monday during a meeting with Manohar in Nagpur.
Raman was appointed COO of the IPL by Lalit Modi in January 2008.
New BCCI president Shashank Manohar had earlier criticized the boards decision retain Raman post the 2013 IPL spot-fixing and betting scandal.