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Climate change and hydropower operations affect hydrological regimes at regional basin scales and impact hydrodynamics and habitat conditions for biota at the river reach scale. The present study proposes a hierarchical modeling framework for predicting and analyzing the impacts of climate change and hydropower on fish habitats. The approach couples multi-scale climate, hydrological, water temperature, hydrodynamic and habitat suitability models and was applied to a reach of the Jinsha River. Flow discharge and water temperature were predicted in the study area for a baseline scenario and three climate change scenarios, and each considered the presence and absence of impacts caused by hydropower operation. The impacts of flow discharge and water temperature variations on spawning and juvenile Coreius guichenoti, an imperiled warm-water fish in the Jinsha River Basin (JRB), were evaluated using a fuzzy logic-based habitat model. The results showed that habitat suitability and available usable area for the fish increased due to climate change, and water temperature rising was the main influencing factor. Water temperature decrease induced by hydropower operation in the spawning periods resulted in the reduction of available habitat area. However, climate change reduced the negative effects generated by hydropower operation, and the available habitat area for the fish would still be expected to increase under the combined impacts of climate change and hydropower operation in the future. It is predicted that water warming, as a result of climate change, is likely to eliminate the spawning postponement effect generated by hydropower operation on Coreius guichenoti as well as other warm-water fish species in the JRB. In contrast, water warming induced by climate change is likely to exacerbate the negative effects of hydropower operation on the spawning activity of cold-water fish species in the JRB. The present study provides a scheme to predict the impacts of climate change and hydropower on other organisms in river ecosystems. The results are beneficial for the development of long-term and adaptive conservation and restoration measures for aquatic ecosystems. (c) 2018 Elsevier B.V. All rights reserved.