The western Pacific Ocean is the global center for marine biodiversity, with high vulnerability to climate change. A better understanding of the spatiotemporal characteristics and potential drivers of compound marine heatwaves (MHWs) and low-chlorophyll (LChl) extreme events is essential for the conservation and management of local marine organisms and ecosystems. Here, using daily satellite sea surface temperature and model-based chlorophyll concentration, we find that the climatological spatial distribution of MHW-LChl events in total days, duration, and intensity exhibits heterogeneous distributions. The southwest sections of the South China Sea (WSCS) and Indonesian Seas are the hotspots for compound events, with total MHW-LChl days that are more than 2.5 times higher than in the other sub-regions. Notably, there is a trend toward more frequent (> 4.2 d/decade), stronger (> 0.5), and longer-lasting (> 1.4 d/decade) MHW-LChl occurrences in the WSCS. The occurrence of compound MHW-LChl extremes exhibits remarkable seasonal differences, with the majority of these events transpiring during winter. Moreover, there are generally statistically significant increasing trends in MHW-LChl events for all properties on both seasonal and inter-annual timescales. Furthermore, we reveal that the total days of compound MHW-LChl extremes are strongly modulated by large-scale climate modes such as the El Niño-Southern Oscillation and Dipole Mode Index. Overall, pinpointing MHW-LChl hotspots and understanding their changes and drivers help vulnerable communities in better preparing for heightened and compounded risks to marine organism and ecosystems under climate change.