Abstract: We conducted a survey on the structure and distribution of fish communities in the Suwalong to Hutiaoxia section of Jinsha River in October-November 2012, May-June 2013, May-June and October-November 2019. The results showed that 17 fish species were distributed in the study area, of which 11 species were indigenous and six species were exotic. Schizothorax wangchiachii, Schizothorax dolichonema, Schizothorax kozlovi, and Euchiloglanis kishinouyei were mainly distributed in the main stream of Jinsha River, while Schizopygopsis malacanthus, Gymnocypris potanini firmispinatus, and Triplophysa sp. were more frequently found in the tributaries. The Shannon diversity index, Pielou evenness index, and Margalef richness index of fish species across sampling points ranged from 0.20 to 0.75, 0.18 to 0.39, and 1.44 to 3.37, respectively. Overall, the diversity indices of sampling points in the main stream section of the Jinsha River were higher than that in the tributary section. The fish communities from 2012 to 2013 could be divided into two groups at a level of 70% Bray-Curtis similarity. When the Bray-Curtis similarity reached 55%, fish communities in 2019 could be divided into three groups. Euchiloglanis kishinouyei, Schizothorax dolichonema, and Jinshaia sinensis tended to occur in rapid or torrent sections with high flow rates, while Triplophysa sp. more occurred in slow flowing sections with low flow rates. Schizothorax kozlovi and Schizopygopsis malacanthus tended to occur in wide valley streams. Based on the community structure and distribution characteristics of fish species, we proposed the following measures to protect fish resources, including strengthening the control of alien species, strengthening the planning and design of environmental protection measures for hydropower projects, carrying out habitat restoration, and strengthening aquatic ecological monitoring.