Marine heatwaves (MHWs) are prolonged extreme sea surface temperature events. Under global warming, their frequency, intensity, and duration have increased markedly, threatening the ecological stability of global ocean. Phytoplankton underpin marine primary production, food webs, and the biological carbon pump. Their functional stability during MHWs is key to predicting ecosystem responses to extreme events. Yet a global-scale assessment of this stability under MHWs remains lacking. Here, we identified 42,211,549 MHW events across the global ocean over 1982–2025. Detection was based on NOAA OISST v2.1 sea surface temperature data. We used satellite-derived chlorophyll-a concentrations to examine Functional Overall Ecological Vulnerability (Functional OEV). As complementary measures, we also quantified four functional stability metrics—resistance, resilience, recovery, and temporal stability. Mapping the spatial distributions of vulnerability and four stability metrics revealed that phytoplankton communities in the open-ocean basin regions of the central equatorial Pacific and the North Pacific subtropical gyre exhibited high vulnerability, accompanied by low resistance and recovery. Likewise, coastal upwelling regions of the eastern Pacific—off the west coasts of North America, Central America, and Peru—displayed the same pattern. We grouped the global ocean into four Longhurst biomes: Polar, Westerlies, Trades, and Coastal. MHW intensity and duration effects were detrended via penalized-spline generalized additive model, and biome-level differences in community stability residuals were then quantified and tested. Before covariate control, stability followed a Polar > Westerlies > Trades > Coastal gradient. The Polar biome exhibited stronger Resistance and substantially lower Functional OEV than expected under equivalent MHW forcing, whereas the Coastal biome performed worst across all metrics, with Functional OEV partial effect reaching +0.981, suggesting nearshore ecosystems are disproportionately vulnerable under compounded environmental stressors. Unexpectedly, Polar and Coastal biomes exhibited similarly large fluctuations in temporal stability around recovery trajectories, whereas mid-latitude open oceans displayed the smallest fluctuations. This study shows Under equivalent MHW forcing, polar communities showed highest resistance and lowest functional vulnerability, but their recovery was as temporally unstable as coastal communities. Conversely, coastal communities performed worst across all stability metrics, with disproportionately high vulnerability, marking them as the most threatened functional hotspots. These findings provide a scientific foundation for biome-targeted conservation strategies and for projecting marine ecosystem responses to future climate warming.