Abstract: The issue of reservoir water temperature has gradually become a key topic in the collaborative research on hydropower development and ecological protection. To clarify the water temperature impacts of high-head seasonal-regulating hydropower stations in the mountainous areas of Southwest China, as well as the improvement effects, ecological benefits and economic benefits of stratified water intake measures, this study takes the Pubugou Hydropower Station as a case. It adopts a width-averaged vertical 2D water temperature model to conduct numerical simulation research on the temporal and spatial distribution characteristics of water temperature in the reservoir area and the water temperature impacts of stratified water intake measures. The results show that the water temperature structure of the Pubugou Hydropower Station reservoir area is stratified, with issues of low-temperature water discharge in spring and summer and high-temperature water discharge in autumn and winter. During the fish spawning period from March to August, the discharged water temperature is lower than that of the natural river, with the maximum temperature difference occurring in April (3.3°C). Among the three stratified water intake schemes—front retaining wall, laminated beam gate, and water isolation curtain—the water isolation curtain scheme demonstrates the best improvement effect on discharged water temperature, capable of increasing low-temperature water by 0.5°C in spring and summer and reducing high-temperature water by 0.2°C in autumn and winter. The water isolation curtain scheme integrates ecological and economic benefits, with negligible head loss. If applied to the Pubugou Hydropower Station, it could avoid economic losses of 74 to 185 million yuan per year. The research findings provide technical references for water temperature regulation and management of the Pubugou Hydropower Station and other similar high-head seasonal regulation hydropower stations in southwest mountainous areas, contributing to the joint construction of green hydropower models and the ecological beauty of the Dadu River.