Under ongoing global warming, global coastal upwelling systems are increasingly recognized as potential thermal refugia from marine heatwaves, owing to their ability to transport colder subsurface water to the surface. Here we hypothesized that the upwelling (downwelling) concurrent with marine heatwaves would restrict (deepen) their maximum depth. Mixed-layer heat budget analyses using satellite and reanalysis datasets revealed an intrinsic connection between the seasonally varying upwelling system and marine heatwaves over the Greater Bay Area of China. Notably, upwelling driven by local monsoons and coastal topography appears to limit the vertical extent of marine heatwaves, modulating transitions between surface and subsurface events. Our findings provide a distinct perspective on the role of coastal upwelling in shaping the vertical structure of marine heatwaves. While upwelling regions may still serve as thermal refugia under continued warming, their buffering effect is likely more pronounced for subsurface or bottom marine heatwaves than for surface events.