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Marine heatwaves (MHWs) perturb air–sea CO2 fluxes, but their cumulative impact on the global coastal carbon sink remains poorly understood. Using four observation-based CO2 flux datasets, with priority given to a global coastal product, we find that MHWs enhance net CO2 uptake in global shelf seas by 11.0 ± 1.6% from 1985 to 2020, in contrast to reduced uptake in the open ocean. The enhancement is largely attributable to polar and subpolar shelf seas, where frequent MHWs coincide with sea-ice loss and non-thermal reductions in dissolved inorganic carbon (DIC), outweighing reduced uptake or enhanced outgassing in lower-latitude, warming-dominated regions. Analysis with a global ocean biogeochemical model suggests that the observed DIC reductions are largely linked to enhanced biological carbon fixation. Our findings reveal region-specific MHW impacts on coastal carbon dynamics, highlighting a critical role of high-latitude shelf systems in the global carbon budget under ongoing climate change. This study reveals that marine heatwaves enhance the global coastal carbon sink, driven by polar and subpolar shelf seas through sea ice reduction and biological processes, contrasting with weakened CO2 uptake in the open ocean.