Within a polyculture system of Portunus trituberculatus and Penaeus japonicas (SC), Sinonovacula constricta with low density (SCC₁), medium density (SCC₂) and high density (SCC₃) were raised to construct an integrated aquaculture system of Portunus trituberculatus, Penaeus japonicus, and Sinonovacula constricta, respectively. Monthly samples from the aquaculture system were collected from July to December 2020 to analyze the phytoplankton community structure during aquaculture. Canonical correspondence analysis (CCA) and redundancy analysis (RDA) were used to analyze the relationship between the phytoplankton community structure and environmental factors. The results showed that there were six phyla, 54 genera, and 81 species during aquaculture; species abundance relating to class in descending order was: Bacillariophyta＞Pyrrophyta＞Cyanophyta＞Chlorophyta＞ Euglenophyta＞Cryptophyta. Among them, there were 30 dominant species, mainly including Cyclotella sp., Synedra acus, Stauroneis anceps, Phormidium tenus, Oscillatoria tenuis, and Euglena sp.. Phytoplankton density ranged from 2.23×10⁵ ?28.06×10⁵ cells/L, the biomass was 0.06?21.37 mg/L, the Shannon-Wiener diversity index was 0.90?2.42, the Pielou evenness index was 0.31?0.78, and the Margalef richness index was 1.00?2.08. The diversity of phytoplankton was high and this community was stable. The CCA and RDA results showed that water temperature, transparency, and salinity were the main environmental factors affecting the integrated aquaculture systems of Portunus trituberculatus. When the medium (75.0 kg/hm² ) and high densities (112.5 kg/hm² ) of Sinonovacula constricta were mixed in the polyculture system of Portunus trituberculatus and Penaeus japonicus, there was good diversity in the phytoplankton community. Such diversity may achieve the balanced development of phytoplankton and enhance the anti-interference ability of the culture system. This diversity is beneficial to the stability of the comprehensive polyculture system of the Portunus trituberculatus pond.