Abstract: To address the degradation of aquatic habitats caused by extreme drought and small hydropower development in the Yipin River Basin, this study selected the reach from the Sanqiaowan Hydropower Station to the Baijie Hydropower Station as the research object. A two-dimensional numerical model was established using measured hydrological and topographical data. A nature-like habitat restoration model with shallow-deep pool configurations was constructed using submerged, orthogonally arranged spur dikes. The variations in hydrodynamic indicators, including water depth and flow velocity, were analyzed. A fish population dynamics model based on the Leslie matrix was developed to evaluate the recovery of fish populations after habitat restoration under the impact of extreme drought. The restoration effects were validated using field monitoring data of fish resources before and after habitat restoration. The results showed that during the extreme drought event in 2022, when the minimum daily average flow rate was 0.10 m³/s, the water depth in front of and between the spur dikes in the Sanqiaowan water-reducing reach increased from 0.36~0.38 m to 0.43~0.75 m, and the water depth in the Qiaokou Dam water-reducing increased from 0.14~0.47 m to 0.70~1.30 m. Flow velocity increased at the dike heads and decreased between the dikes, forming a regular flow distribution pattern. The extreme drought caused a sharp decline in fish populations, with juvenile fish being the most severely affected; after habitat restoration, fish populations increased significantly. The research results can provide reference for river habitat restoration.