Marine heatwaves and their ecological impacts are commonly characterized using event-mean metrics, yet ecosystems experience these disturbances as time-evolving sequences of physical forcing and biological adjustment. Collapsing these sequences into single values can obscure distinct phytoplankton response trajectories and cannot capture how response timing and physical–biological coupling are changing in a warming ocean. Here, we normalized marine heatwaves to a common lifecycle and quantified global trajectories of sea surface temperature (SST), mixed-layer depth (MLD), and satellite chlorophyll anomalies, showing that similar event-mean chlorophyll anomalies can arise from markedly different temporal pathways. Although the timing of response extrema varied spatially and with event properties, a consistent sequence emerged: mixed-layer shoaling occurred in the early stage, SST peaked near mid-event, and chlorophyll minima followed later, consistent with a delayed biological response to physical forcing. Physical-biological coupling was geographically heterogeneous, with predominantly negative SST–chlorophyll and positive MLD–chlorophyll relationships that varied systematically with latitude. One striking exception occurred in the eastern equatorial Pacific, where surface chlorophyll declined despite mixed-layer deepening. Vertical observations revealed stronger stratification, restricted nutrient supply to the surface, and vertical redistribution of chlorophyll. Thus, surface observations alone are insufficient to resolve the underlying mechanism highlighting the need for a three-dimensional perspective. Under global warming, the strongest mixed-layer shoaling and chlorophyll minima have shifted toward earlier lifecycle stages, while SST–chlorophyll correlations have become more negative. Marine heatwave impacts on phytoplankton are therefore better understood as phase-dependent, regionally heterogeneous, and vertically structured trajectories rather than static surface anomalies.