Giant hydropower development is a major human disturbance activity in the watersheds of southwestern China, which has a great impact on the socio-ecological systems of ecologically fragile areas. The changing direction and pattern of socio-ecological system evolution are complex and non-linear and involve major national needs such as ecological protection and restoration, energy security, economic development, and rural revitalization. Therefore, there is an urgent need to strengthen research on the evolution and driving mechanisms of socio-ecological systems in watersheds. By summarizing the progress and shortcomings of current research, we propose countermeasure suggestions such as strengthening a long-term monitoring and analysis of ecosystem evolution; conducting in-depth research on the laws and driving mechanisms of the watershed socio-economic evolution; improving the valuation of watershed ecological assets and ecological compensation mechanisms; and constructing the theory and methods of watershed socio-ecological system coupling. This study will provide the scientific and technological support for the future sustainable development of fragile ecological zones.