Abstract: To investigate the community structure of macroinvertebrates in the Ili River, fourteen sampling sites were selected representing four habitat types, i.e., natural habitat, damaged habitat, under-dam habitat and protected area in July 2014 and 2015. A total of 81 macroinvertebrate taxa were collected, belonging to 39 families and 10 orders, of which, 75 species (93.8%) were aquatic insects, and 2 species (2.5%) were mollusks, and 3 species (3.7%) were oligochaete. The natural habitat had higher density, species richness, EPT richness and biodiversity of macroinvertebrates than others, and the under-dam habitat displayed the lowest values. Results of Redundancy Analysis (RDA) explained 54.1% of the cumulative variance of species data. Monte Carlo permutation tests for the first axis and overall canonical ordination were significant, indicating that distribution of macroinvertebrates were mainly regulated by flow rate, conductivity, water temperature and altitude (F=2.28—4.34, P<0.05).