The macroinvertebrate community structure and environmental factors were surveyed in 23 sampling sites in the Lhasa River Basin in August 2017. A total of 41 macroinvertebrate species were collected, of which, 35 species (85.4%) were aquatic insects, 2 species (4.9%) were mollusks, 3 species (7.3%) were annelids, 1 species (2.4%) was nematomorpha. The average number of species was 8 from all sites, there were significant differences in the dominant species composition, the main dominant species were Baetis spp., Tipula sp., Hydopsyche sp., Brachycentrus sp., Limnodrilus sp., and Chironomus sp. The average density of macroinvertebrate species was 362 ind/m². The macroinvertebrate community structure was evaluated by using biodiversity indices (including the Margalef species richness index, Shannon-Wiener index, and Pielou index). The level of biodiversity indices were relatively low, and the average value of each index was 1.18, 1.32, and 0.49, respectively. The Pielou index and Biotic Index were used to assess the water quality. The two results of assessment, respectively, showed that 30.3% and 56.5% of sampling sites were moderately polluted or heavily polluted. Canonical correspondence analysis revealed that macroinvertebrate community structure was heavily determined by levels of altitude, COD_Cr, sulfides, pH, TP and TN.