An investigation was conducted on the phytoplankton community structure, abundance, functional groups, and diversity indices in the Lhasa River in August 2017; subsequently, canonical correspondence analysis (CCA) was used to study its relationships with environmental factors. The results showed that Bacillariophyta (60.4%) was the dominant phytoplankton, the second was Chlorophyta (20.8%), and the remaining 18.8% was composed of a variety of species. The average abundance was 3857 cells/L; Bacillariophyta, Cyanophyta, and Chlorophyta accounted for 94.6%, 3.1%, and 2.3%, respectively. Few species and low abundance are special characteristics of the phytoplankton community structure in the Lhasa River. The most dominant species of phytoplankton was Nitzschia sp. In total, 15 types of phytoplankton functional groups were identified:MP, D, and P were dominant, comprising 93% of all groups, with other phytoplankton functional groups accounting for the remaining 7%. The diversity indices of Margalef, Shannon-Wiener, and Pielou's evenness were 1.41, 1.77, and 0.5, respectively. The diversity index was not significantly different between the main stream and branches when analyzed using one-way analysis of variance. CCA indicated that the pH, chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) were the main environmental factors that influenced phytoplankton assemblages and that pH, TN, and TP were the main environmental factors that influenced the functional groups.