Abstract: According to the environmental characteristics of different seasons, this study conducted surveys on phytoplankton and water environment in Longhe River and Ruxi River during spring (March), summer (July), autumn (September), and winter (November) in 2021. The results showed that 111 phytoplankton species were collected in Longhe River, belonging to 6 phyla. A total of 142species of phytoplankton were collected from Ruxi River, belonging to 7 phyla. According to Padisak theory, 23 phytoplankton functional groups were identified in both Longhe River and Ruxi River. The seasonal changes of dominant functional groups of phytoplankton in Longhe River were as follows: spring (B, L_O, MP, X1)→summer (D, J, S_N, T_B)→autumn (D, J, MP, P, T_B)→winter (B, D, MP, T_B). The seasonal changes in Ruxi River were as follows: spring (B, D, X1, X2)→ summer (G, J, S1, X2)→autumn (S1, G, P)→ winter (D, J, MP, S1). The backwater areas of the Longhe River and Ruxi River were affected by the impoundment of the Three Gorges Project, leading to greater similarity in phytoplankton functional group composition. According to the redundancy analysis of phytoplankton functional groups and environmental factors, water temperature (WT), dissolved oxygen (DO), pH, ammonium nitrogen (\rmNH^+_4 -N), and phosphate (\rmPO^3-_4 -P) were the main factors affecting the phytoplankton distribution in the two rivers. This study provides a theoretical basis for protecting the aquatic ecosystem of the Yangtze River.