The taxonomic analysis of phytoplankton functional groups can accurately reflect the impacts of changes in water quality on the hydrobiological community. In order to explore the effects of sediment dredging on the phytoplankton community and aquatic ecosystem of the Shuangqiao River in the Chaohu basin, the environmental factors of the river and the structure and functional groups of the phytoplankton community during sediment dredging period of the Shuangqiao River from June 2017 to March 2018 were investigated. The results showed that sediment dredging greatly reduced the concentration of nitrogen and phosphorus in the Shuangqiao River, but the river still retained its middle-eutrophic state after sediment dredging. In total, 23 phytoplankton functional groups were identified: M, H1, H2, MP, S1, L_O, X2, X1, J, F, N, G, X3, C, D, Y, W1, L_M, E, T, S_N, K, and P. The phytoplankton functional groups were dominated by the M functional group (mainly comprised of Microcystis spp.) and the MP and P functional groups (mainly composed of Diatoms). Sediment dredging had little effect on the species composition of the phytoplankton in the Shuangqiao River. However, the density and biomass of algae declined significantly after sediment dredging. The phytoplankton diversity index has also improved. Redundancy analysis (RDA) and Pearson analysis were used to explore the relationships between phytoplankton functional groups and the major environmental factors of the Shuangqiao River. A significant relationship between phytoplankton functional groups and environmental factors was found. Among them, the dominant functional groups of phytoplankton in the Shuangqiao River changed from M, MP, P, W1, and Y before sediment dredging to C, F, J, M, MP, P, and Y after sediment dredging. At the same time, the reduction of nitrogen concentrations caused by sediment dredging projects has had a great impact on the phytoplankton functional groups of the Shuangqiao River. This study shows that the sediment dredging project of the Shuangqiao River has had a positive effect by improving the ecological functions of the phytoplankton community and reducing the degree of water pollution.