Abstract: To understand the structure and its driving factors of macroinvertebrate community, two surveys were conducted in the Anning River and its tributaries in wet season (July and August 2016) and dry season (January and February 2016). Furthermore, sampling was also performed monthly from July 2015 to June 2016 in the tributaries of the Anning River. As a result, a total of 122 species of macroinvertebrates were collected, which belonged to 115 genera of 5 phyla. Among them, aquatic insects (109 species) were dominant taxa. The densities and biomass of macroinvertebrate community were much higher in the tributaries than those in the mainstream both in the wet and dry seasons, and were much higher in the dry season than those in the wet season both in the mainstream and tributaries. All through the year, the dominant species in the tributaries were Baetis sp., Simulium sp., Epeorus sp., Baetiella sp., Peltoperlidae spp. and Ephemerella sp. Temporal variability of macroinvertebrates showed that the highest density was in December and the lowest one in July; while the highest biomass was in January and the lowest one in July. Canonical correspondences analysis (CCA) indicated that substrate type and altitude were the key factors driving the macroinvertebrate distribution in the wet season, whereas flow velocity, altitude and water temperature were the significant driving factors in the dry season. In addition, monthly variations of macroinvertebrate structure in the tributaries were relative to the ecological factors such as water temperature and conductivity. Overall, this study provides a scientific basis for the studies and conservation of biodiversity in high altitude areas.