Two cruises were carried out in the summer and winter of 1998 to study coupled physical-chemical-biological processes in the South China Sea and their effects on phytoplankton stock and production. The results clearly show that the seasonal distributions of phytoplankton were closely related to the coupled processes driven by the East Asian Monsoon. Summer southwesterly monsoon induced upwelling along the China and Vietnam coasts. Several mesoscale cyclonic cold eddies and anticyclonic warm pools were identified in both seasons. In the summer, the upwelling and cold eddies, both associated with rich nutrients, low dissolved oxygen (DO), high chlorophyll a (Chl a) and primary production (PP), were found in the areas off the coast of central Vietnam, southeast of Hainan Island and north of the Sunda shelf, whereas in the winter they form a cold trough over the deep basin aligning from southwest to northeast. The warm pools with poor nutrients, high DO, low Chl a, and PP were found in the areas southeast of Vietnam, east of Hainan, and west of Luzon during the summer, and a northwestward warm jet from the Sulu Sea with properties similar to the warm pools was encountered during the winter. The phytoplankton stock and primary production were lower in summer due to nutrient depletion near the surface, particularly PO4. This phosphorus depletion resulted in phytoplankton species succession from diatoms to dinoflagellates and cyanophytes. A strong subsurface Chl a maximum, dominated by photosynthetic picoplankton, was found to contribute significantly to phytoplankton stocks and production.