The phytoplankton primary productivity is a great basis to evaluate the structure and function of aquaculture ecosystem, which qualify important significance for fishery resources exploitation. In this study, we measured the phytoplankton primary productivity among shrimp (Litopenaeus vannamei) ponds during the aquaculture periods in the Minjiang River estuary, Southeast China. The results showed that the gross primary production (GPP), respiration (R_P) and net primary production (NPP) of phytoplankton among ponds over the shrimp aquaculture period varied from 619.99 to 9498.67, 1003.16 to 7063.33, and -4179.50 to 6362.96 mg O₂/(m²·d) respectively, with mean values of (4386.22±409.72), (3607.53±150.27) and (778.68±260.16) mg O₂/(m²·d) respectively. Overall, the mean GPP, R_P and NPP decreased significantly among the three ponds in the order:PondⅡ > PondⅢ > PondⅠ. The phytoplankton primary productivity demonstrated a clear seasonal pattern, with an increasing trend with time. Multiple stepwise regression analysis showed that nitrogen nutrient and chlorophyll-a were the major impact factors of the spatiotemporal variations of phytoplankton primary productivity in shrimp ponds. Our results highlighted that the importance of considering the spatiotemporal variations in primary productivity in improving the accuracy of large-scale estimation of phytoplankton primary productivity in coastal aquaculture pond.