This study shows that the response of satellite-observed chlorophyll (CHL) to eddy motion varies seasonally in the South China Sea (SCS). The spatial pattern of the CHL anomaly composite for eddies is a dipole in summer and a monopole in winter, indicating that sea surface CHL is largely regulated by the horizontal rotational velocity of the eddy in summer and by eddy pumping and trapping in winter. The dipole pattern for anticyclonic eddies was confirmed by in situ observations, which also show that the dipole pattern is mainly restricted to the mixed layer. The underlying mechanism was further investigated with a coupled physical–biogeochemical model. The key driver leading to the seasonal variation of the eddy effect is found to be the seasonal variation of the mixed layer depth. In summer when the mixed layer is shallow, the monopole nutrient change induced by eddy is restricted to the subsurface. The sea surface CHL distribution is thus mostly affected by eddy advection. In winter, the deepening of the mixed layer mixes the nutrients from subsurface where eddy significantly changes the nutrient levels, allowing the monopole pattern to be observed in the sea surface CHL anomaly.