In order to explore the spatial and temporal characteristics of the phytoplankton community structure and its influencing factors in Shanghai rivers, the water quality and phytoplankton community structure at 44 river channel sites in a central urban area, new town area, and rural area in Shanghai were investigated from September to October 2018 (autumn) and July to August 2019 (summer). The results showed that:① Chlorophyta was the dominant phyla during the autumn and summer, and was followed by Cyanobacteria and Bacillariophyta. Cyanobacteria dominated the phytoplankton community in terms of density. The number of species and density of phytoplankton were 24% and 2.77 times higher, respectively, than those during the summer and autumn. The dominance of