Marine heatwaves (MHWs) are receiving fast-growing attention due to their devastating ecological and socioeconomic impacts under global warming. Despite studies on the response of phytoplankton abundance to MHWs, their effects on phytoplankton size structures (PSS), a crucial property of phytoplankton community, are poorly understood. Here, we present a global assessment of PSS changes during MHWs based on multi-satellite observations. We find that MHWs tend to increase the dominance of smaller-size phytoplankton in mid-low latitudes, while shifting PSS towards larger-size species in high latitudes. Compared with the high-latitude oceans, PSS are more susceptible to MHWs in mid-low latitudes. Hotspots of PSS shifting to smaller species are observed in the tropical oceans, the eastern boundary upwelling systems, the mid-latitude transition zones, mainly due to reduced nutrient availability associated with changes in oceanic processes. In contrast, the shift of PSS to larger size classes in the high-latitude oceans are likely attributed to increased light exposure during MHWs. The potential recovery time of these PSS disturbances exhibits marked spatial heterogeneities and suggests a more elastic phytoplankton community during MHWs in mid-low latitudes. These results extend our understanding of the phytoplankton responses to MHWs and have important implications for global fisheries and carbon cycling.