It is of great significance to reveal the mechanism of phytoplankton community structure in aquatic ecosystem for effective prevention of harmful algal blooms and scientific management of aquatic ecosystem. In order to reveal the mechanism and its driving factors in Lake Poyang, one of the river-connected lakes in the middle and lower reaches of the Yangtze River, the phytoplankton and its functional groups and the environmental factors of 38 sampling sites were investigated in August 2020 in the lake. A total of 91 species in 59 genera from 7 phyla were detected, among which Chlorophyta (27 genera and 46 species), Bacillariophyta (13 genera and 22 species) and Cyanobacteria (8 genera and 11 species) accounted for 50.5%, 24.2% and 12.1% of the total species, respectively. Phytoplankton can be divided into 23 functional groups, with N, G, P, W1 and L_O as the dominant ones, indicating that Lake Poyang was at the risk of eutrophication. The phytoplankton community structure varied significantly between in the bay and the main channel area of the lake, with higher values of Shannon-Wiener diversity index, Simpson diversity index and Pielou evenness index of phytoplankton in the bay area (Mann-Whitney U test, P<0.001). Correlation analysis between the community distance and the environmental and geographic distances showed that both environmental filtering and spatial dispersal constraints influenced phytoplankton communities and its functional groups. Variation partitioning analysis, C-score analysis and modified stochasticity ratio analysis further clarified that the deterministic process (environmental filtering) was dominant and had a greater influence on the functional groups. Constrained ordination analysis showed that turbidity, COD_Mn and conductivity were the most important environmental factors driving the change of phytoplankton community structure in Lake Poyang, while temperature, conductivity and COD_Mn were the main environmental factors influencing the community structure of phytoplankton functional groups in Lake Poyang.