Low-head dams and small hydropower developments are widely distributed in global rivers because of their high cost-efficiency and smooth implementation. However, these installations have great ecological impacts on native fish communities due to the loss of longitudinal river connectivity. Although dam removal and fishway construction are effective measures to mitigate river fragmentation, research on their effects on fish communities remains limited to date. In this study, we investigated fish community dynamics in a mountainous tributary of the Jinsha River–Heishui River following dam removal, fishway construction, and fishway renovation. Our fish sampling data from 2018 to 2023 yielded 6137 fish belonging to 25 species, 12 families, and 3 orders. The native fish community predominantly represented the typical fish fauna of the Qinghai-Tibetan Plateau, primarily including the genus Schizothorax and the families Sisoridae and Nemacheilidae. Representative fish species in the Heishui River demonstrate notable adaptations to cold water, high altitude, and rapid flow environments. After removing the Laomuhe Dam, upstream fish abundance increased sharply, but species richness slightly decreased in the short term. Fishway construction significantly enhanced species richness and abundance and reduced the difference between the upstream and downstream fish communities from the Songxin Dam. However, the subsequent fishway renovation altered the dominance of fish species, with marginal changes in community structure and abundance. Variations in fish community dynamics in the river channel and fishway structure can be attributed to differences in ecological guilds (e.g., flow preference and thermal regime) and environmental factors (e.g., flow discharge, water temperature, and water depth). The present study provides insight into the significance of mitigation measures for the impact of dams on mountainous rivers in southwest China through ecological assessment and guides for decision-making in the conservation and restoration of specific fish communities.