Abstract Understanding how the vertical structure of marine heatwaves (MHWs) influences ecosystems remains limited. Here we investigated subsurface‐intensified (Type‐1) and surface (Type‐2) MHWs in tropical oceans using reanalysis data sets. Type‐1 MHWs occur most frequently and are concentrated near the equator, with a threefold greater median vertically integrated cumulative anomaly (VICA) than Type‐2 MHWs. Although both types are primarily modulated by ENSO, their underlying mechanisms differ: Type‐1 MHWs are more closely linked to oceanic dynamics, whereas Type‐2 MHWs are strongly influenced by atmospheric heating. Critically, the annual mean VICA of Type‐1 MHWs increased significantly during 1993–2020, driven by a deepening of the anomaly penetration depth rather than by intensification per unit depth. Ecologically, both types of MHWs reduce surface chlorophyll‐a; however, Type‐1 MHWs suppress deep chlorophyll maxima by exacerbating nutrient limitation, posing more severe vertical threats to phytoplankton biomass. These findings highlight the distinct nature and increasing risk of subsurface MHWs.