Abstract: Phytoplankton is an essential component for the functioning of material cycle and energy flow which accounts for half of earth’s primary production. Meanwhile, phytoplankton community structure and distribution are important indicators of water environment and its quality. Identifying the main factors driving phytoplankton community structure is essential for better understanding and therefore managing freshwater ecosystem. Hence, we investigated phytoplankton community structure, morphology-based functional groups and temporal and spatial distribution of these groups among Lake Xiannü and inflow rivers during 2014—2015. There were 82 species of 7 phyla recorded, including 15 species of Cyanophyta, 33 species of Chlorophyta, 23 species of Bacillariophyta, 3 species of Pyrrophyta, 5 species of Euglenophyta, 2 species of Cryptophyta and 1 species of Chrysophyta. The average phytoplankton density and biomass were in ranges of 7.95×10⁶—2.19×10⁹ ind./L and 10.52—792.91 mg/L, respectively. Non-flagellated, with siliceous exoskeletons phytoplankton (Group Ⅵ, diatom) was the dominant species in river habitat in spring and autumn. Unicellular flagellates of medium to large phytoplankton (Group Ⅴ, Cryptophyta and Pyrrophta) was the dominant species in lake zones. Although biomass of Group Ⅵ phytoplankton was relatively high in different habitats, large filaments with aerotopes phytoplankton (Group Ⅲ) and large mucilaginous colonies (Group Ⅶ), such as Cyanophyta, increased significantly between summer and autumn. Analysis of the relationship between phytoplankton morphology-based functional groups and environmental factors found that the biomass of Group Ⅴ and Ⅵ was affected by the TN and TP concentration in winter and spring. In summer and autumn, phytoplankton of Group Ⅲ and Ⅶ were affected by multiple factors including water temperature, turbidity and TN and TP concentrations.