The operation of cascade reservoirs has profoundly affected the quality of fish spawning habitats. This study examined three representative spawning reaches within the National Nature Reserve for the Rare and Endemic Fishes in the Upper Reaches of the Yangtze River, selecting two target fish species with distinct spawning characteristics for each reach. An eco-hydrological model was employed to assess spawning habitat quality under different reservoir operation modes from 2013 to 2023. The findings indicate that for drifting-egg-spawning fish species, the weighted usable area (WUA) remained relatively low during the non-ecological scheduling stage, and the ecological scheduling implemented in the cascade reservoirs has significantly enhanced the WUA for these species. In contrast, no significant improvement was observed for sticky-egg-spawning fish species. By establishing WUA-discharge relationships for target species in each study reach, it was found that drifting-egg-spawning fish exhibit significantly higher flow requirements compared to sticky-egg-spawning fish. Based on the average WUA values under natural hydrological conditions, suitable Xiangjiaba Reservoir releases for target fish species were proposed.