Abstract This study investigates the interannual variability of marine heatwaves (MHWs) in the Bay of Bengal (BOB) associated with the Indian Ocean dipole (IOD) from 1982 to 2021. The results revealed a significant positive correlation at the 95% confidence level between the IOD and MHW days in the central bay at the peak of the IOD in autumn. During positive IOD (pIOD) events, the central bay experienced more MHW days in autumn, with an average increase of 7.4 days. The increased MHW days in the central bay could be primarily attributed to the enhanced net heat flux (TQ), which is 9.7 times the contribution of ocean dynamic processes (horizontal advection + entrainment). The reduced latent heat flux loss and enhanced shortwave radiation due to the anomalous atmospheric low-level high pressure associated with the pIOD account for 63% and 50%, respectively, of the anomalous enhanced TQ, while the longwave radiation and sensible heat flux make smaller contributions of −20% and 7%. In addition, thermocline deepening in the southwestern bay, caused by this anomalous high pressure and associated anticyclonic wind anomalies, favors the occurrence and persistence of MHWs by reducing the mixed-layer cooling rate. In addition to the influence of the IOD, El Niño–Southern Oscillation mainly affects MHWs from winter to the following summer, which confirms the result of a previous study.