In order to alleviate the impact of greenhouse gas emission on climate change, the green hydropower assessment that centers on the harmonious development between clean hydropower and eco-environment has become a research hotspot. In accordance with the current situation of research on green hydropower in China and abroad, a complete, independent, representative, comparable and implementable indicator system is proposed in this paper, and the green hydropower evaluation indicators and their thresholds are explored by analyzing the environmental, economic and social impacts of the construction and operation of cascade hydropower projects in typical areas of the upper reaches of the Yangtze River from perspectives of flood control, ship transport, energy, eco-environment, ecological compensation for immigrants and cultural and landscape compensation. International green hydropower certification system and the present technical standards in China are taken as basis. Moreover, by choosing typical cases as the pilot ones, an evaluation system of ecological protection, economic benefits and social influence that covers the full life circle of the hydropower projects is established to guarantee an environmental-friendly construction of hydropower projects in China and to promote the sustainable development of clean hydropower energy in China.