Water temperature has been recognized as one of the important hydrological indicators. However, changes in water temperature are going to threaten the sustainability of aquatic ecosystems owing to the climate change and the increased anthropogenic activities. While some of the world's largest cascade reservoirs have been developed in the upper reaches of the Changjiang River, it remains unclear about the combined effects of these reservoirs and climate changes on the water temperature and aquatic ecosystems. In this study, long-term water temperature and meteorological data (1989-2019) from Yibin-Chongqing segment of the Changjiang River were used to investigate the impacts of meteorological factors and Jinshajiang River cascade reservoirs on downstream water temperature, as well as to reveal the responses of fish spawning time to the water temperature changes in the National Nature Reserve for the Rare and Endemic Fishes located in the upper reaches of the Changjiang River. The major results of this study are: The average annual water temperatures in the study areas increased significantly over the last 30 years, with an increase of 0.5-1.1℃; After the impoundment of Xiangjiaba-Xiluodu cascade reservoir, the annual water temperature processes were delayed about 36, 13 and 7 days at three stations along the reservoir, respectively. The “cooling effect” and “warming effect” in the lower reaches were significant in spring and autumn-winter due to the impoundment of the cascade reservoirs, with the maximum increased and decreased ten-day mean water temperature of 1.8-3.7℃ and 1.3-3.6℃, respectively. Therefore, the “warming effect” was greater than the “cooling effect”; The annual variations of water temperatures were mainly caused by the cascade reservoirs and the inter-annual variations were mainly caused by climate changes, which clearly showed an increasing trend; The time to reach the optimum spawning water temperature for important fish nearby the Xiangjiaba Hydrometric Station was delayed by 30-40 days after the reservoir impoundment, in the order of Ancherythroculter nigrocauda > Leptobotia elongate, Coreius guichenoti, Procypris rabaudi > Jinshaia sinensis > Acipenser Dabryanus > Myxocyprinus asiaticus. Notably, the overlaps of the ecological niches for fish populations were increased. The results of the study may provide guidance to mitigate the impacts of hydropower development on aquatic ecology.