In this study, the data of macroinvertebrates from 2010 to 2019 were systematically analyzed, to provide more comprehensively basic information for the macroinvertebrate diversity assessment in the upper and middle reaches of Jinsha River and the biodiversity research and protection of the high-altitude rivers. The results showed that aquatic insects were dominant in the composition of macroinvertebrates in the upper and middle reaches of Jinsha River, mainly composed of Diptera, Ephemeroptera, Trichoptera and Plecoptera, while mollusks, mainly Basommatophora were lower. At the family level, the Baetidae, Chironomidae, Heptageniidae and Perlidae were the common taxa in the whole study area, among which Chironomidae and Baetidae were common both in the main stream and tributaries as well as in the wet and dry seasons. The community structure in the main stream and tributaries was significantly different, which was not affected by the wet season and dry season, meanwhile the community structure in the wet and dry seasons was significantly different, which was not limited by the main stream and tributaries. Small minnow mayflies (Baetis, Cloeon dipterum, Baetiella and Baetidae), common stoneflies (Paragnetina, Perlidae) and hydropsychids (Hydropsyche) were the key taxa that caused the significant differences in community structure between groups. The macroinvertebrates in the whole study area showed a high nestedness, and the distribution pattern of macroinvertebrates in dry season was more nested than in wet season, and that in the tributaries was more nested than in the main stream. The taxa richness and density & biomass were higher in dry season than in wet season, and higher in the tributaries than in the main stem. On the contrary, the β diversity was higher in wet season than in dry season, and higher in the main stream than in the tributaries. Based on the observation data in the past decade, the taxa of macroinvertebrates in Jinsha River Basin were relatively rich, with 148 observed taxa, and the estimated taxa number based on statistics was about 200. However, according to the single survey, the taxa number in a single station in the dry and wet seasons of the main stream was very low, indicating that the community structure was very simple, and the taxa number in a single station of tributaries was relatively high, indicating that the community structure was relatively complex.