In recent years, more frequent marine heatwaves (MHWs) in the South China Sea (SCS) have affected surface chlorophyll-a (Chl-a). Traditional linear statistical methods have limited capacity to identify the contributions of multiple highly interrelated physical drivers in complex oceanic systems. To address this limitation, we applied the Synergistic–Unique–Redundant Decomposition (SURD) method to investigate MHW-related Chl-a anomalies from 1998 to 2024. Analyses reveal a marked regional contrast during summer MHWs, with positive Chl-a anomalies in the northern SCS and negative anomalies in the western SCS. Although summer thermal extremes in both regions were linked to similar anomalous atmospheric circulations associated with the western North Pacific subtropical high, the local physical mechanisms controlling Chl-a responses differed. In the South Vietnam upwelling region, weakened wind forcing reduced Ekman pumping and vertical transport, limiting surface cooling and nutrient replenishment to the euphotic zone, thereby contributing to negative Chl-a anomalies. In the Pearl River Estuary, enhanced incident shortwave radiation promoted rapid surface warming, while weakened wind-driven export favoured the nearshore retention of low-salinity plume water. The SURD results indicate that retained plume water enhanced surface layer stratification and likely increased nutrient supply, allowing plume retention to act synergistically with cumulative heat stress and supporting positive Chl-a anomalies. However, unresolved optical and biological processes in the Pearl River Estuary introduce uncertainty into the inferred nutrient pathway. These results suggest that besides thermal forcing, Chl-a responses to MHWs in marginal seas are also significantly affected by regional physical pathways.