Marine extreme temperature events pose severe threats to marine ecosystems. While existing research on extreme temperature events in the Bay of Bengal (BoB) has largely focused on sea surface conditions and large-scale processes, the occurrence and drivers of subsurface extremes remain poorly constrained. To address this gap, an extensive dataset combining uninterrupted mooring measurements (2008–2016) with diverse remote sensing products is utilized to elucidate the nature and forcing mechanisms of extreme temperature events within the northern Bay of Bengal (NBoB). The results reveal a clear vertical decoupling of subsurface marine heatwaves (MHWs) and cold spells (MCSs) from surface events. Surface extremes are principally forced by air-sea heat fluxes and remotely modulated by El Niño-Southern Oscillation through atmospheric teleconnections. In contrast, subsurface events are predominantly driven by mesoscale eddies, with over 50% of MHWs and MCSs co-occurring with anticyclonic and cyclonic eddies, respectively. Furthermore, we find that the occurrence of subsurface eddy-associated MHWs is modulated by the synchronization of La Niña with negative phases of the Indian Ocean Dipole, during which anticyclonic eddy activity becomes anomalously active, leading to an increased frequency and enhanced intensity of these MHWs. This vertical dichotomy in governing mechanisms, with atmospheric processes dominating at the surface and eddy dynamics controlling the subsurface, advances our understanding of extreme temperature dynamics in tropical seas and provides crucial insights for predicting marine ecosystem responses under climate change.