Phytoplankton chlorophyll a (Chla), primary production (PP), and nutrient uptake rates are fundamental and important parameters in marine biogeochemical studies. However, the relationships between them are associated with much uncertainty that reflects gaps in basic understanding of ecosystem dynamic. In this study, we simultaneously measured PP and nitrate assimilation (NA) along with estimated concentrations of nutrients, particulate organic carbon concentrations, phytoplankton Chla, pigments, and carbon biomass in the dynamic shelf ecosystems of the East China Sea (ECS) on four cruises during different seasons. There were large spatial gradients of these parameters, and seasonal patterns of phytoplankton Chla and PP varied between water masses. The results of this study and previous work indicated that seasonal variations of Chla and PP were similar in coastal waters but opposite in off‐shelf waters. During summer in off‐shelf waters, there were patches of high PP and NA associated with low Chla concentrations; this pattern was reversed in the winter. We suggest that there is a global tendency for PP and Chla patterns to be out of phase. This asynchrony is reflected mainly in the seasonal variations of C:Chla ratios driven by the combined influences of light, temperature, and nutrients. Stronger grazing pressure by microzooplankton in summer likely contributed to the high production but low biomass in the ECS. The significant correlation between PP and NA suggested that variations of PP in the ECS were driven largely by nitrate uptake, which may be inhibited by high ammonium concentrations in the Changjiang River plume.