Abstract: In order to learn the fish diversity in some important branches of Three Gorges Reservoir, the investigation was carried out in the 2015 and 2016  respectively. All important branches can be divided into 4 types: <50 km, 50-100 km,100-300 km, and >1 000 km, and each of them was set to 4, 6, 8, 8 sampling sections respectively. A total of 685.5 kg catches was captured and 35507 samples were measured, 121 species of fish were identified, belonging to 9 order, 22 family and 78 genus, and Cypriniformes and Cyprinidae were the dominated order and family in this research, 68 species were endemic to China, 26 species were endemic to the upper reaches of the Yangtze River, and 9 species were exotic species. The number of total and endemic fish species to China and the upper reaches of the Yangtze River in Xiaojiang River were the largest compared to other rivers, and the Qijiang River followed. The investigation results showed that fish ecological types were mainly viscous eggs, benthic fishes, carnivorous and omnivorous in the study area; there were significant differences in the average taxonomic distinctness Δ+ between rivers greater than 1000 km and others by using t-tests (P<0.05), there were no significant differences in the variation in taxonomic distinctness Λ+ among 4 types of rivers with t-tests (P>0.05), and indicated that there were no significant correlations between Δ+, Λ+ and river length using Pearson correlation test (P>0.05); the main economic fish species included Cyprinus carpio, Carassius auratus, and Pseudobagrus nitidus. In conclusion, taking measures such as prevention introduced species escape and study on artificial reproduction of rare fish should be benefit for protecting fish diversity resources.