The upstream post-dam movement strategies of fish constitute an important basis for evaluating habitat suitability in dam-affected river reaches. In particular, how the typical abrupt hydraulic characteristics of mountainous rivers influence post-dam upstream migration behaviour remains an urgent question to be addressed. In this study, two representative loach species from the Heishui River in the Jinsha River basin, the red-tailed loach Paracobitis variegatus and the short-bodied loach Paracobitis potanini, were selected as target species. Fish resources of the target species were investigated using net-capture surveys, and radio frequency identification (RFID) technology was applied to evaluate the post-dam upstream migration performance of the two loach species. A quantitative evaluation model of post-dam upstream migration performance for loaches was developed by coupling hydrological and hydrodynamic factors of the reservoir area, in order to identify the key factors influencing post-dam upstream migration performance and to establish response curves between upstream migration success and these key factors. The results showed that: (1) the fishway passage rates of the two loach species in 2022, 2023, and 2024 were 22.92%, 9.01%, and 7.00%, respectively; (2) after dam passage, loaches exhibited different proportions of habitat selection, with 85% remaining in the near-dam reservoir area, 15% continuing upstream to 0.7 km above the dam, and no loaches migrating to 1.3 km above the dam; (3) the dominant factors affecting post-dam upstream migration performance were fish species, river discharge, and river water temperature; (4) post-dam upstream migration success was significantly negatively correlated with river discharge and water temperature (P < 0.05), and the upstream migration success of P. potanini was significantly higher than that of P. variegatus (P < 0.05); and (5) surveys of post-dam loach distribution and substrate characteristics indicated that loaches were mainly distributed in areas characterized by mixed cobble and silt substrates. This study provides an important reference for ecological operation of small hydropower stations and post-dam habitat restoration in the Jinsha River basin.