A cruise was taken in October 2015 to determine phytoplankton size structure near Zhangzidao Island and adjacent waters. The surface and bottom distribution of size-fractioned phytoplankton and its correlation with environmental factors were examined. The concentration of total chlorophyll a, microplankton (>20μm), nanoplankton (2-20μm), and picoplankton (0.45-2μm) were measured in the surface and bottom layers. In the surface layer, the total chlorophyll a concentration ranged between 0.52-1.25μg/L with an average of 0.76μg/L. The corresponding concentration for microplankton, nanoplankton, and picoplankton were 0.03-0.81, 0.33-0.91, and 0-0.09μg/L with averages of 0.19, 0.53, and 0.03μg/L, contributing 23.77%, 72.26%, and 3.98% of the total chlorophyll a, respectively. In the bottom layer, total chlorophyll a concentration ranged between 0.14-1.5μg/L with an average of 0.46μg/L, which was primarily made up by microplankton and nanoplankton, which ranged between 0.04-1.04 and 0.08-0.47μg/L with averages of 0.22 and 0.24μg/L, contributing 41.46% and 58.50% to the total chlorophyll a, respectively. The surface chlorophyll a concentration was significantly higher than that in the bottom layer. The vertical distribution of nanoplankton was homogeneous, whereas the nanoplankton and picoplankton tended to be more abundant in the surface layer. The concentration of picoplankton was lower than that of the other two size classes throughout the entire water column in autumn. Significantly positive correlations were found between nanoplankton concentration and salinity in the surface layer, using Pearson's correlation analysis. In the bottom layer, significantly positive correlations were found for several pairs of parameters, including the total chlorophyll a and phosphate concentration, microplankton and phosphate and silicate concentrations, and nanoplankton and temperature. Temperature, salinity, and phosphate and silicate concentrations were important factors affecting the size structure of phytoplankton near Zhangzidao Island and adjacent waters.