Based on data collected from 31 sampling sites during June and August 2018 in the three ordered rivers (the tributaries of the Anning River, the Anning River, and the lower Yalong River), fish assemblages in the region were investigated regarding their spatial variations, and their relationship with environmental factors. In total, 48 species were collected, with 47 being native and one being exotic. Among them, one was classified as endangered. Fish species diversity increased first and then decreased, reaching its peak in the mid-order river. Obvious variations were found in fish assemblages depending on the stream order. There were three site-groups: one covering the tributaries of the Anning River, one covering the Anning River, and one covering the lower Yalong River. From low- to high-order rivers, the alterations of key species within the fish communities exhibited a turnover pattern. The fish assemblages in the low-order river were primarily dominated by Nemacheilida, whereas the mid-order river and the high-order river displayed a dominance of Gobioninae and Cultrinae, respectively. These spatial variations might be primarily impacted by altitude and water depth. Moreover, this study highlights the critical role of mid-order rivers in sustaining fish diversity within dendritic stream networks of mountain rivers.