The western South China Sea (WSCS) exhibits intense mesoscale eddy activity, especially in summer. However, the influence of the eddies on regional ecosystems is not well understood. By analyzing historical in situ observations, satellite-derived near-surface chlorophyll (CHL) data and eddy data, we investigated the composite response of CHL to eddies in the WSCS. The results show that eddies decrease CHL in the WSCS and that nearly half of this decrease is attributed to the activity of anticyclonic eddies during summer when they are much more energetic than cyclonic eddies. A comparison between local and nonlocal eddies suggests that the CHL response to the eddies is dominated by local dynamics rather than being trapped and transported from neighboring regions. In situ observations provide evidence that intense convergence and downwelling in anticyclonic eddies deepen the mixed layer depth and subsurface CHL maximum depth. The decreased nutrients in the euphotic layer inhibits the growth of phytoplankton, resulting in a weakened subsurface CHL maximum (by 54%) and decreased CHL in the entire euphotic layer (by 41% for the upper 100 m). Considering the greater number and area of anticyclonic eddies compared with cyclonic eddies, eddy activity might cause an upper ocean CHL decrease of~7% in the WSCS in summer. This study demonstrated that the response of CHL to eddies in the WSCS differs in both spatial distribution and seasonal variation from those in other subregions of the SCS, emphasizing the importance of considering regional variability in eddies and large-scale environments when evaluating the biogeochemical influences of eddies.Plain Language Summary Mesoscale eddies, both local and nonlocal, enrich the circulation system in the western South China Sea (WSCS), giving rise to complex regional biogeochemical environments. To gain insights into the role of eddies in regional ecosystems, we investigated the composite near-surface chlorophyll (CHL) anomalies within thousands of eddies in the WSCS. The results show a noticeable near-surface CHL decrease induced by the eddies, and nearly half of this decrease is attributed to the activity of anticyclonic eddies in summer. During this period, intense downwelling in anticyclonic eddies results in much deeper and weaker subsurface CHL maximums than those in cyclonic eddies, as well as the backgrounds. This study demonstrates that the CHL response to eddies in the WSCS differs in both spatial distribution and seasonal variation from those in the northern and eastern SCS, emphasizing the importance of considering regional variability in eddies and large-scale environments when evaluating the biogeochemical influences of eddies.