Abstract: Ecological compensation is an important means to coordinate the contradiction between socio-economic development and eco-environmental protection in the Yangtze River Economic Belt.At present, ecological compensation in the Changjiang River Basin is faced with inadequate integrity and systematicness, lacking compensation standard basis, an unsound market system, and unclear responsibilities and rights.According to the strategic need for protection and development in the new era, ecological compensation in the Changjiang River Basin needs to have a richer connotation.It is urgent to explore the key scientific issues including the spatial-temporal relationship between socio-economic development and eco-environmental protection, quantitative accounting and spatial transformation of ecological service, diversified ecological compensation framework and long-term operation mechanism, and regional pilot demonstration and overall advance.Besides, it is needed to provide scientific support and policy recommendations for the overall framework of ecological compensation in the Changjiang River Basin by innovating institutional mechanisms, improving technological systems, strengthening legislative guarantees, and fostering market subjects.