Surveys have been conducted to investigate the spatial and temporal distribution of size-fractionated phytoplankton and other environmental variables in Sanggou Bay in four seasons for the period covering April 2017 until January 2018. Results showed that chlorophyll a concentration in the surface and bottom layers ranged from 0.74 to 3.27 µg/L and from 0.81 to 3.66 µg/L, respectively, with average values of (1.90±1.28) and (2.01±1.29) µg/L, respectively. There were significant differences in chlorophyll a concentration (P<0.01) and spatial distribution between seasons. In spring, microphytoplankton was the most abundant, accounting for 54.05% and 58.08% of the total phytoplankton in the surface and bottom layers, respectively. In summer, picophytoplankton was the most abundant, accounting for 24.46% and 20.70% of total cholorophyll a in the surface and bottom layers, respectively. In autumn, picophytoplankton accounted for 35.88% and 40.77% of total chlorophyll a in the surface and bottom layers, respectively. The contribution of picophytoplankton was low in winter and spring but increased significantly in summer and autumn. Redundancy analysis (RDA) results show that temperature is the main environmental factor affecting the size structure of phytoplankton. Dissolved oxygen had a significant effect on the percentage of picophytoplankton to total phytoplankton. The percentage of nanophytoplankton correlated with NO2 and NH4. There was a significant positive correlation between temperature and the percentage of microphytoplankton. This study provides basic knowledge for understanding the size structure of phytoplankton and estimating the carrying capacity of filter-feeding shellfish in the aquaculture ecosystem in Sanggou Bay.