A survey of fish community structure was conducted in six sections of the Ili River, China from 2012 to 2019. The results showed that there were 29 species of fish in the Ili River, most of which are belonging to Cyprinidea. Compared to the record at the end of the last century, the composition of fish species has changed. Schizothorax argentatus Kessler, Barbus brachycephaius Kessler, Carassius auratus gibelio (Bloch), Hypophthalmichthys molitrix (Cuvier et Valenciennes) and Misgurnus bipartitus (Sauvage et Dabry) did not appear in the present survey, especially Schizothorax. argentatus Kessler,there is no capture record in the fish resource investigation by far. Channa argus (Cantor) and Silurus meridionalis Chen, which were not captured in historical studies, were presented in this study. Totally, the occurrence and number of alien fishes have increased. According to the analysis of the fish community structure characteristics, there was low diversity in the Ili River, China. It was significantly different between the main stream and the tributary in fish community structure. At present, the main alien fishes are Cyprinus carpio Linnaeus, Hemiculter leucisculus (Basilewsky) and Carassium auratus (Linnaeus) in the Ili River, China. Using Maximum entropy modelling (MaxEnt) to predict the potential distribution of C. carpio, H. leucisculus and C. auratus in the Ili River, and compared with the fish occurrence, it revealed that the potential distribution was consistent with the actual distribution in C. carpio and H. leucisculus. But C. auratus has spread to the tributary compared with the potential distribution. The alien fish have strong adaptability, furthermore, the absence of controlling and prevention at the beginning of their introduction, made the size of their population and habitat were growing larger in the Ili River, which has low fish diversity. The invasion of the alien fishes will introduce a great threat to endemic fishes. To restrain the spread of alien fish, and maintain the ecological security of the Ili River, China, the life history and invasive mechanism of the alien fish should be paid a great attention, especially for C. auratus that has undergone niche drift. The climate and hydrological of the habitat at the upstream tributaries, especially for native fish spawning, feeding and wintering, should be monitored. The long-term monitoring of fish resources and the changes of fish community structure in the Ili River is needed. The artificial propagation and releasing of native fish should be taken. Meanwhile, it is necessary to exercise strict control over the alien fish entrainment with import and export trade or artificial releasing.