Marine heatwaves (MHWs), periods of abnormally high sea surface temperature (SST), have substantial impacts on marine ecosystems. Large marine ecosystems (LMEs) cover ~22% of the global ocean but account for 95% of global fisheries catches. Yet how climate change affects MHWs over LMEs remains unknown because such LMEs are confined to the coast where low-resolution climate models are known to have biases. Here, using a high-resolution Earth system model that resolves ocean mesoscale eddies and improves the capability to reproduce MHWs compared with the coarse-resolution models, we apply a “future threshold” that considers MHWs as anomalous warming above the evolving long-term warming and find that the future intensity and annual days of MHWs over the majority of the LMEs remain higher than in the present-day climate. These increases in MHWs suggest that even if species could adapt fully to the future mean warming, risks from marine heatwaves to coastal ecosystems are substantial.