Evaluation of the relative influences of environmental and spatial processes in structuring aquatic phytoplankton metacommunities is an essential step for understanding the species spatio-temporal distributions. To reveal the relationships between community structures of phytoplankton and the environment as well as clarify the driving mechanism of environmental factors and spatial diffusion limiting factors on phytoplankton community structure in Zhelin Reservoir, Lake Poyang Basin, the phytoplankton and water quality physicochemical characteristics of 33 sampling sites were investigated and analyzed in October 2020. A total of 122 species belong to 7 genera were identified, with 62 species in 34 genera were Chlorophyta, accounting for 50.81% of the total species, followed by Bacillariophyta with 27 species in 11 genera. The dominant species of phytoplankton in Zhelin Reservoir are Pseudoanabaena, Planktolyngbya and Raphidiopsis of Cyanophyta and Synedra of Bacillariophyta. The cell abundance of phytoplankton in the Zhelin Reservoir varied from 0.93×10⁶ to 172.12×10⁶ cells/L with an average of 95.42×10⁶ cells/L, and the biomass varied from 0.95 to 22.35 mg/L with an average of 9.35 mg/L. The phytoplankton biodiversity index in the upstream Xiuhe tributary area was significantly higher than that in the center of the reservoir area and the reservoir bay area, while no significant difference in the phytoplankton biodiversity index between the center of the reservoir area and the reservoir bay area was found. The phytoplankton community structure in the Xiuhe tributaries of Zhelin Reservoir was separated from that in the center reservoir and reservoir bay, and the differences were mainly affected by water transparency, electrical conductivity, ammonia nitrogen and nitrate nitrogen. The results of variation partitioning showed that the spatial diffusion limiting effect was dominant in driving the phytoplankton community structure in Zhelin Reservoir.