Background: As the most widely distributed river form in the world, meandering river is of great significance for stabilizing the physical structure of the river and maintaining ecosystem. To quantitatively study the positive effects of meandering rivers, the Chishui River, a natural tributary of the Yangtze River in Southwest China, is selected as the research area, and two typical river sections with different meandering degrees are selected as the research objects. Methods: Based on the field survey data, the local endemic fish Procypris rabaudi (Tchang) is considered the object fish, and a hydrodynamic model was used to simulate the distribution of water depth and flow velocity in certain river reaches at different flows. By introducing the weighted usable area (WUA) and hydraulic unit diversity index, combined with the suitability curves of the study species, the hydraulic characteristics and habitat suitability changes of two river reaches under different flows are summarized and analyzed, and the hydrogeomorphological process of the studied river section is generalized. Results: With the change in discharge, a positive correlation is observed between the maximum velocity and depth of the meandering river and the discharge, whereas the WUA and hydraulic unit index of the meandering river have relatively small changes. Under low discharge, the distribution of pool–riffle sequences can be seen in the meandering reach, which is essential to improve the ecological suitability and stability of the river. Conclusions: This study provides scientific sustentation for river restoration and fish conservation.