Marine heatwaves (MHWs) are episodic warm SST events that severely affect marine ecosystems. How global warming impacts MHWs over Large Marine Ecosystems (LMEs)—covering 22% of the ocean but 95% of fisheries—remains unclear due to model biases. Using a high‑resolution eddy‑resolving model, we found that atmospheric rivers (ARs) can intensify MHWs by suppressing ocean cooling. Applying a future threshold (warming above long‑term mean SST rise), we project that MHW intensity and annual days over most LMEs will remain higher than present. MHWs also occur subsurface; globally, subsurface MHWs increase due to rising mean temperatures and enhanced variability. Historically, maximum intensity is at ~100 m depth, but shifts surfaceward under warming. Removing the trend, subsurface increases exceed surface ones, especially in LMEs. Concurrent surface–subsurface events rise tenfold. Our study underscores heightened threats, as subsurface heatwaves reduce vertical refuge for marine organisms.