Abstract: This study investigated annual variations of fish communities in different sections along the longitudinal gradient of the near-natural river based on the data collected from 2007 to 2016. A total of 133 fish species, belonged to 7 orders, 20 families and 84 genera, were collected. Among these species, Acipenser dabryanus and Myxocyprinus asiaticus have been enlisted as class Ⅰ and II protected species in China, while other 36 species endemic to the upper Yangtze River. The number of fish species increased along the longitudinal gradient, which increased from 47 in Chishui Town Section to 90 in the Chishui City Section and to 120 in the Hejiang County Section. Cluster analysis and non-metric multidimensional scaling (nMDS) ordination analysis revealed that the fish communities in all sections were varied significantly over time. The relative abundance of large and medium-sized economic fishes, such as S. sinensis and O. sima, declined continuously, while the small-sized fishes such as H. labeo, S. argentatus and R. giurinus showed the opposite trends. Additionally, the abundance of some endemic fish species, such as H. tchangi and C. guichenoti, declined markedly. The induced reasons included local overfishing, navigation, channel regulation and hydropower development, as well as changes of aquatic environment in the mainstream of the upper Yangtze River. In order to effectively protect fish stocks, it is recommended to strictly manage fisheries and water activities. Further strengthen long-term monitoring and timely detect changes in fish mix structure.