The seasonal succession of function groups in benthic diatom and its relationship with environmental factors were investigated in Ruxi River, an important branch of Three Gorges Reservoir. Results showed that 168 species of benthic diatoms belonging to 27 genus, 8 families were found in this river, and these species were categorized to 8 functional groups including B, C, D, L_O, MP, P, X3 and T_B during three different water periods for low, level and high water period, and MP was absolutely dominant. Redundancy analysis suggested that seasonal succession of functional groups in the benthic diatom was mainly determined by nitrite, conductivity, phosphate, permanganate index and water temperature.