The upper reaches of the Yangtze River (YR) constitute the largest group of hydropower cascade projects in the world. The construction of cascade hydropower systems has a significant impact on the flow regimes and sediment transport in rivers, ultimately affecting fish spawning. Previous studies have examined the effects of fluctuating flow and water temperature on spawning; however, insufficient attention has been paid to their effects on sediment transport. This study analysed changes in runoff and sediment load (SL) at the Xiangjiaba hydrologic station (XJB) and Zhutuo hydrologic station (ZT) in the upper reaches of the YR over the past 60 years. Based on the indicators of hydrological regimes and sediment transport, we used the generalized additive models (GAM) to investigate the effects of cascade hydropower operations from 2009 to 2018 on the spawning abundance of Coreius heterodon (C. H) in the upper YR Fish Reserve. Following the operation of cascade hydropower, the SL and sediment concentration decreased by 56.8% and 56.6%, respectively, while the median size of the bed-material load demonstrated an initial thinning trend followed by subsequent coarsening. In addition, the frequency of the high-flow pulse increased by 32.1%, whereas the peak flow and duration of the high-flow pulse decreased by 41.2% and 62.6%, respectively. However, no significant changes were noted in the indicators of the flooding process. The decrease in sediment transport and changes in the flow regime led to a reduction in the spawning abundance of C. H. Reductions in sediment transport and changes in high-flow pulses caused by cascade hydropower can negatively affect C. H spawning, and SL is the most important indicator of impacts on spawning abundance (contribution of 77.7%). These findings are critical for evaluating the long-term impacts of cascade hydropower on fish habitats.