The spatial and temporal patterns of river meanders play a crucial role not only in shaping the hydrogeomorphic properties of channels and floodplains but also in ascertaining the suitability of fish habitats for river ecological conservation. This study evaluates hydrodynamic features and fish habitat quality in six highly sinuous bend sequences along the Black River in China’s Qinghai plateau. The ecohydraulic model system was used to simulate hydrodynamics, habitat suitability, and sediment transport to determine the habitat quality of the highly sinuous bend sequences. The results have successfully identified differences in the suitability of various bends for fish spawning. Bend 1 was found to be the most suitable among all bends, while bends 5 and 6 were deemed unsuitable specifically during higher flood flows. Cases 3 and 4 were discovered to be highly suitable for fish habitat under normal discharge scenarios. Conversely, cases 5 and 6 were the least suitable, with cases 5 and 6 exhibiting the worst habitat quality, with HSI values nearing zero under high discharge. The study concluded that regulated discharge conditions could support fish spawning in these sinuous bends, with lower flood flows promoting habitat suitability and higher flood flows fragmenting habitat quality. The findings highlight the importance of diverse hydrodynamic and geomorphic conditions in creating suitable fish habitats across varying flow conditions, offering insights into the conservation and management of mountain rivers to protect endangered fish species and aquatic organisms.