Abstract: The middle reaches of the Jialing River have the most intensive hydropower projects, which significantly impact the development of phytoplankton communities in the lower reaches. Based on this, this study conducted a seasonal survey on the reaches in 2019 to investigate the current status of the phytoplankton community structure and analyze the impact of environmental changes on the composition and quantity of phytoplankton species. Specifically, the following research findings have been made. First, there is a certain degree of pollution in the investigated reaches, especially reflected in the exceeding of the total phosphorus (TP) content. Second, a total of 196 species, which belonged to 91 genera in 7 phyla, were identified, and their annual mean of total density was 4.23×106cells/L. Moreover, the dominant phyla were ordered as Chlorophyta > Bacillariophyta > Cyanophyta. Compared with the historical data, the richness and relative density of Bacillariophyta decreased, while those of Chlorophyta and Cyanophyta increased, suggesting the eutrophication trend of the investigated reaches. Furthermore, the results of the biodiversity index also show a certain degree of pollution in the reaches. Third, the results of Classification and Regression Tree showed that phytoplankton might proliferate in reaches with abundance TP, high pH, and moderate secchi depth. Fourth, according to the Redundancy Analysis, all dominant species of Chlorophyta identified were positively correlated with the water temperature and TP, while only Cyclotella with the highest dominance in the Bacillariophyta species preferred the higher TP and lower flow velocity (FV). Furthermore, the Cyanobacteria dominated by filament strains that adapt to a certain FV preferred high water temperature and were positively correlated with the FV. It is concluded that the current eutrophication and low-speed flow of the Jialing River are the main reasons of the Bacillariophyta that prefer clean water and high FV gradually losing their dominance, and the increasing dominance of Chlorophyta, Cyanophyta and Cyclotella that prefer high nutrition and low FV. For different power station reservoirs, there is a risk of Cyanophyta and Chlorophyta blooms in summer with high temperatures, and a Bacillariophyta bloom dominated by Cyclotella in early spring with low temperatures. It is recommended that the water environment of the reaches should be comprehensively managed to reduce the eutrophication, and the sluices need to be opened in time to increase the FV of the reservoir, thus reducing the potential risk of algal blooms.