Abstract: Nearly 90% of the hydropower resources in the Yangtze River basin are concentrated in the upper reaches of the Yangtze River. The cascaded hydropower dams and river channelization have caused habitat fragmentation and loss of fish diversity, which has aggravated the contradictions between hydropower development and environmental protection. This paper collected data on aquatic reserves (i.e. natural reserves and aquatic germplasm resources conservation zones) and cascade dams in the upper reaches of the Yangtze River, and vectorized the data in ArcGIS. Taking into account the diversity, richness and distribution of fish, we analyzed the changes in fish resources and the problems in the construction and management of the upper reaches of the Yangtze River. Therefore, several strategies have been proposed to reduce the conflicts between hydropower development and aquatic ecosystem protection, including conducting reserve census, evaluating management effectiveness of the protected areas for spatial optimization of the reserve networks, implementing the ecological restoration of essential fish habitats, implementing the rescue action plan for the upper Yangtze endangered endemic fish, establishing an efficient ecological compensation mechanism, and strengthening scientific monitoring and related research. These recommendations will provide a scientific basis for the coordinated development of hydropower exploitation and river ecological protection in the upper Yangtze River.