Abstract: To understand the fish community structure and its variation in the Four Major Chinese Carps Aquatic Germplasm Resources Reserve in Chongqing section of the upper reaches of the Yangtze River (after this referred to as the protected area) at the beginning of the "Ten-Year Fishing Ban",this study investigated the fishery resources and collection of environmental factors in the protected area from May to June and from October to November 2023. A total of 56 fish species were collected,which belonged to 6 orders,16 families,and 43 genera. Among the species,9 were endemic to the upper reaches of the Yangtze River (16.07%).In addition,there were 8 alien fish species (14.29%). The community composition was mainly composed of bottom fish,quiet and slow-flowing fish,sink-laying fish,and omnivorous fish. The small fish such as Pseudobrama simoni,Hemifilter leucisculus,and Squalidus argentatus was the dominant species in the protected area. The Shannon-Wiener index,Margalef index,Pielou index,and Simpson index ranged from 1.49 to 2.80,4.14 to 5.69,0.43 to 0.79,and 0.53 to 0.90,respectively. The species diversity index was significantly correlated with permanganate index,flow velocity,transparency,and substrate type (P<0.05). Cluster analysis and non-metric multidimensional scaling analysis (NMDS) showed that the fish community types in the river section of the protected area were divided into three groups,i.e.,group one: Luoqi and Mudong,group two: Xiamenkou,Linshi,and Wujianghekou,group three: Zhenxi. Redundancy analysis (RDA) showed that flow velocity and water depth were the key environmental factors that significantly affected the spatiotemporal distribution of fish communities in the protected area (P<0.01). The abundance biomass comparison curve (ABC curve) analysis showed that the fish community structure in the Xiamenkou section was relatively stable,while in other sections was moderately to severely disturbed. Compared with the historical data,the fish community in the protected area had undergone significant changes. This study systematically analyzed the characteristics of fish community structure,spatio-temporal changes and the relationship with environmental factors in the protected area. This study supplemented the existing data on the current status of fish resources and provided a scientific basis for fishery resources management and initial ecological assessment of the "Ten-Year Fishing Ban" in the study area.