Marine heatwaves (MHWs) are devastating extreme ocean temperature events whose frequency and severity have surged under global warming, threatening marine ecosystems and fisheries. Yet the fundamental mechanisms that control their intensity and persistence remain incompletely understood. Here, using a submesoscale-permitting global model simulation validated by long-term observational and reanalysis data, this study reveals a previously overlooked submesoscale feedback that exerts a critical control on MHW severity. It is demonstrated that the submesoscale-induced vertical heat flux suppresses the intensity and persistence of atmospheric-driven MHWs in winter via a negative feedback mechanism. Enhanced air-sea net heat flux strengthens stratification and shoals the mixed layer, weakening submesoscale vertical heat transport by 19.4%, reducing MHW intensification by 18.1%, and accelerating decay by 21.7%. This missing regulatory mechanism indicates that models ignoring submesoscales likely overestimate MHW severity, with critical implications for future climate projections.