Abstract: Strengthening the protection of the eco-environment of the Yangtze River is related to the overall situation of socio-economic development in the Yangtze River Basin, which is not only an objective requirement for maintaining the eco-environmental safety of the Yangtze River Basin, but also an important part of implementing major central policies. Relying on the first phase of the joint research project on the eco-environmental conservation and restoration of the Yangtze River, the problems existing in the water eco-environment of the basin were diagnosed, the causes were analyzed, and the policy suggestions for strengthening the conservation and restoration of the water eco-environment were put forward. The main water eco-environmental problems in the Yangtze River Basin included: the decline of the river connectivity and the shrinking of the area of lakes and wetlands caused by the development of resources in the basin; the relatively large intensity of pollutant discharge, and the common deterioration of water quality during the flood season common; the degradation of water ecosystems, the frequent occurrence of lake blooms and red tides in the Yangtze River estuary and the decline in fishery resources, which meant a long way to go with the protection of rare and unique aquatic organisms; the prominent water environmental risk problems, and the frequent occurrence of sudden water pollution accidents. The causes of water eco-environmental problems in the Yangtze River Basin mainly included: the contradiction between the accelerated process of urbanization and population agglomeration and the shortcoming of the environmental infrastructures; the synergy of eco-environmental governance was still insufficient; the control and governance of territorial space was not in place; and the climate change brought new challenges. Accordingly, some countermeasures and suggestions were proposed, including strengthening territorial space management and control at the watershed level and implementing "Three Lines and One List" policy; making up for the shortcomings of infrastructure and deepening pollution prevention and control; promoting the overall planning of "Three Waters" and continuing to carry out ecological restoration; strengthening policy coordination and promoting diversified co-governance; strengthening institutional innovation and enhancing scientific and technological support capabilities, in order to provide a reference for continuing to fight the battle of protection and restoration of the Yangtze River, and for promoting the Yangtze River Economic Belt to become the main battlefield of China′s ecological priority and green development.