The ocean has absorbed approximately 90% of the excess heat related to anthropogenic greenhouse gas emissions, fundamentally reshaping its thermodynamic structure and modulating global climate change. Although the response of multi-scale ocean dynamics—from basin-scale circulation to mesoscale eddy—to this forcing is increasingly documented, the climatic imprint of submesoscale eddies with horizontal scales of 1–30 km has persisted as a blind spot in climate science due to observational and computational limitations. In this study, by applying an innovative submesoscale parameterization scheme to observational datasets between 1993 and 2024, we find a significant intensification trend of submesoscale vertical heat flux (VHF_sm) in the global ocean. The increasing hotspots are concentrated in western boundary currents and the Antarctic Circumpolar Current, where trends reach ~10 W·m^-2/decade—an order of magnitude greater than corresponding trends in net air-sea heat flux. This amplification is mechanistically linked to mixed-layer deepening. Heat budget analysis reveals that enhanced VHF_sm contribute substantially to the accelerated upper-ocean warming, thereby having broad implications for the climate system. These results highlight the crucial role of submesoscale eddies in upper-ocean warming and underscore the necessity of incorporating submesoscale parameterization into climate models to enhance the accuracy of climate projections.