Dam removal is considered an effective measure to solve the adverse ecological effects caused by dam construction and has started to be considered in China. The sediment migration and habitat restoration of river ecosystems after dam removal have been extensively studied abroad but are still in the exploratory stage in China. However, there are few studies on the ecological response of fishes at different growth stages. Considering the different habitat preferences of Schizothorax prenanti (S. prenanti) in the spawning and juvenile periods, this study coupled field survey data and a two-dimensional hydrodynamic model to explore the changes in river morphology at different scales and the impact of changes in hydrodynamic conditions on fish habitat suitability in the short term. The results show that after the dam is removed, in the upstream of the dam, the riverbed is eroded and cut down and the riverbed material coarsens. With the increase in flow velocity and the decrease in flow area, the weighted usable area (WUA) in the spawning and juvenile periods decreases by 5.52% and 16.36%, respectively. In the downstream of the dam, the riverbed is markedly silted and the bottom material becomes fine. With the increase in water depth and flow velocity, the WUA increases by 79.91% in the spawning period and decreases by 67.90% in the juvenile period, which is conducive to adult fish spawning but not to juvenile fish growth. The changes in physical habitat structure over a short time period caused by dam removal have different effects on different fish development periods, which are not all positive. The restoration of stream continuity increases adult fish spawning potential while limiting juvenile growth. Thus, although fish can spawn successfully, self-recruitment of fish stocks can still be affected if juvenile fish do not grow successfully. This study provides a research basis for habitat assessment after dam removal and a new perspective for the subsequent adaptive management strategy of the project.