Many native fish species in the Tarim Basin are endangered, owing to the invasion of alien fish species over the past decades. To better understand how to protect native fish and control the spread of alien fish, the number of alien fish species in the Tarim Basin and their potential ecological effects on native fish species should be assessed. In the present study, we used Jaccard's Index of similarity to investigate the homogenization of fish fauna between the Tarim Basin and associated regions. Furthermore, we adopted the fish autecology matrix to test whether invasive fish would be able to spread widely in the Tarim Basin in the near future. These data were collected from the literature and from field investigations performed in recent years. Our results showed that a total of 63 fish species have been recorded in the Tarim Basin, including 19 native and 44 alien species. The introduction of alien fish species increased species, genus, and family diversity. However, the G-F diversity index (the ratio of genus diversity index and family diversity index) has decreased. The introduction of alien fish to the Tarim Basin is suggested to have changed the species composition from simple and highly differentiated to complicated and poorly differentiated. Moreover, among 44 alien species, 39 (68.2%) were originally from the middle and lower Yangtze River, 7 (15.9%) were originally from the Ertix River, and 7 (15.9%) were originally from America, Europe, and other regions of Asia. We also found that the index of similarity of fish fauna between the Tarim Basin and associated regions significantly increased before and after the introduction of alien species (P < 0.01), indicating that alien species caused homogenization of the fish fauna within the studied regions. Furthermore, the fish autecology matrix revealed that alien fish species can be well adapted to the habitats of the Tarim Basin, and can cause the decline of native fish species through predation and competition. Therefore, control measures against alien fish should be implemented and/or intensified in order to protect the native fish species of the Tarim Basin.