The ecological environment effects and regulations of the hydropower project have been the hot spots of the international water conservancy scientific research for a long time.The construction and operation of reservoir in Southwestern China,which belongs to the typically ecological vulnerable area,will inevitably change the hydrological processes of rivers,sequentially influencing the biogeochemical behaviors of biogenic elements and the corresponding material field,energy field,chemical field and biological field.Consequently, the ecological function of river ecosystem will be seriously affected by the hydropower development.Based on the present situation of fragile ecology in Southwestern China,two key scientific issues were proposed in this project:1) the evolution and cumulative effects of the material and energy flow process in river under the condition of hydropower development in Southwestern China;2) the disturbance effects of high dams and large reservoirs on the important organism and habitats in river as well as the responses mechanisms of the ecological system.Additionally,three key technical problems that need to conquer urgently were raised:1) multi-objective ecological and hydrological processes regulation and engineering technologies of the hydropower cascade development;2) key technologies of the important fish protection and habitat restoration in the case of hydropower cascade development;3) protection and recovery technologies to maintain the ecological system stability of the large river basin.Lastly,three key technical problems were divided into four frontier research aspects and outlook:1) conducting the researches of ecological influencing mechanisms and restoration following the progressive levels of courses with "abiotic level (water,sand,salt,temperature)-biotic level (microorganisms,algae,zoobenthos,rare and endemic fish)-system level (aquatic habitat,bank slop transition zone,water-land coupling system,basin)";2) illustrating the effects of basin cascade reservoirs (group) on the biogeochemical process of biogenic elements as well as its cumulative effects and building the coupling model with multi-dimension and multi-levels;3) revealing the disturbance law of the keystone species and their habitats in river posed by cascade high dams and large reservoirs,analyzing the response processes of ecological system to the hydropower development,developing the technologies of fish habitat restoration and spanning the high dam;4) the research of river health problem has been transformed from concept to application,and their application in river ecological restoration and regulation are the directions of future development.