The growth of indigenous fish resources in the source region of a river is dependent upon the protection and sustainable development of suitable habitats, and the dual effects of climate change and hydropower generation have a major impact on hydrodynamic conditions and living conditions in these habitats. Against a background of climate warming, an agent-based model was established using MIKE3 software and was applied to the source region of the Yellow River. Within the study area, water depth, flow velocity, water temperature, and fish distribution in fish habitats before and after implementation of an ecological scheduling scheme in the hydropower stations were compared. In this paper, the Weighted Usable Area (WUA) method was used to evaluate the habitat suitability before and after construction of the dam in order to study the impact of changes in the hydrology and water environment in the source area of the Yellow River on the survival of the indigenous fish Gymnocypris eckloni Herzensten, 1891 and its eggs, and appropriate solutions were proposed. The results showed that the spawning period of G. eckloni (Gymnocypris eckloni Herzensten) will be delayed and egg hatching will face higher risks due to the negative —effects of low water temperature caused by hydropower generation. Water warming induced by global warming is expected to eliminate this negative influence, and the inhabitable area for fish is expected to increase. This study can provide a reference for evaluating sustainable development of the whole river ecosystem under conditions of climatic change and hydropower engineering operations.