Tropical oceans vitally regulate the global climate and nurture diverse marine ecosystems. Marine heatwaves (MHWs) – warm extremes in ocean temperatures – have been increasingly detected worldwide over recent decades, raising concerns about their potential intensification in tropical oceans with far-reaching consequences. Yet, changes in tropical MHWs remain highly uncertain across climate models. Our analysis of satellite observational data reveals a significant decline in the mean intensity of surface MHWs by 3-11% across tropical oceans since the 1980s. Utilizing ocean reanalysis data and climate model simulations with ~0.1° resolution, we demonstrate that this decline in tropical MHW intensity results primarily from decreased mesoscale sea surface temperature (SST) variability (< ~1000 km), except in the El Niño-Southern Oscillation (ENSO) dominated eastern Pacific region. Heat budget analysis shows that advection by mesoscale eddies is a key driver of tropical MHWs. However, this vital process has weakened owing to declining SST gradients and reduced mesoscale eddy activity in tropical oceans. Our study highlights the pivotal role of mesoscale eddies in regulating MHW dynamics in a warming climate. This finding points to the promising potential for improved prediction of future changes in MHWs and their impacts on climate and biodiversity with refined model resolutions.