Marine heatwaves (MHWs) are extreme oceanic warm water events (above 90th percentile threshold) that significantly impact the marine environment. Several studies have recently explored the genesis and impacts of MHWs though they are least understood in the tropical Indian Ocean. Here we investigate the genesis and trend of MHWs in the Indian Ocean during 1982–2018 and their role in modulating the Indian monsoon. We find that the rapid warming in the Indian Ocean plays a critical role in increasing the number of MHWs. Meanwhile, the El Nino has a prominent influence on the occurrence of MHWs during the summer monsoon. The Indian Ocean warming and the El Nino variability have synergistically resulted in some of the strongest and long-lasting MHWs in the Indian Ocean. The western Indian Ocean (WIO) region experienced the largest increase in MHWs at a rate of 1.2–1.5 events per decade, followed by the north Bay of Bengal at a rate of 0.4–0.5 events per decade. Locally, the MHWs are induced by increased solar radiation, relaxation of winds, and reduced evaporative cooling. In the western Indian Ocean, the decreased winds further restrict the heat transport by ocean currents from the near-equatorial regions towards the north. Our analysis indicates that the MHWs in the western Indian Ocean and the north Bay of Bengal lead to a reduction in monsoon rainfall over the central Indian subcontinent. On the other hand, there is an enhancement of monsoon rainfall over southwest India due to the MHWs in the Bay of Bengal.