Although the South China Sea (SCS) exchanges water constantly with the western Philippine Sea, its nutricline is much shallower and its chlorophyll level in surface waters is twice as high. Analysis of CZCS-SeaWiFS data and shipboard data reveals a strong seasonality of chlorophyll in the SCS in three upwelling regions. A three-dimensional numerical model with coupled physics and biogeochemistry is developed to study the effect of monsoonal forcing on nutrient upwelling and phytoplankton growth in the SCS. The model has a horizontal resolution of 0.4° in the domain 2–24.8°N and 99–124.6°E and 21 layers in the vertical. The circulation is driven by monthly climatological winds. The nitrogen-based ecosystem model has four compartments: dissolved inorganic nitrogen (DIN), phytoplankton, zooplankton and detritus. The chlorophyll-to-phytoplankton ratio depends on light and DIN availability. The biological equations and parameters are taken from previous modeling studies of the Sargasso Sea. The model simulates the nitrate profile, the strong subsurface chlorophyll maximum, and the primary production in the central basin with reasonable success. It also generates intense chlorophyll patches in the monsoon-driven upwelling regions northwest of Luzon and north of the Sunda Shelf in winter and off the east coast of Vietnam in summer. The results are in reasonable agreement with shipboard observations and CZCS-SeaWiFS data. The primary production derived from SeaWiFS data shows a strong peak in winter and weak peak in summer with an annual mean of 354 mg C m−2 d−1 for the whole basin. The modeled primary production displays seasonal variation resembling the trend derived from SeaWiFS data, but the magnitude (280 mg C m−2 d−1) is smaller by 20%. The model also predicts an export fraction of 12% from the primary production in the euphotic zone.