Abstract The tropical Indian Ocean (IO) exhibits persistent biases in sea surface temperature (SST) climatology across Coupled Model Intercomparison Project Phase 6 (CMIP6) models, particularly during boreal winter. These biases manifest as a meridional dipole with warm SSTs in northern tropics and cool SSTs in south. Surface wind induced by interhemispheric SST gradient could intensify southward Ekman transport and reshape the shallow meridional overturning circulation (SMOC). Over the10°S–20°S region, the downward motion of SMOC leads to anomalous subsurface warming, while enhanced evaporation drives surface cooling—weakening vertical thermal structure. Over the equator–10°S, despite favorable upwelling conditions, subsurface remains warm. We attribute this to an overly strong simulation of Indonesian Throughflow, which suppresses the cooling effect of SMOC upwelling. Our results highlight the crucial role of SMOC in connecting the SST bias and subsurface thermal state in climate models and emphasize the need to constrain tropical IO air‐sea interactions for improving SST simulations.