Water environment protection is a key to maintain the Yangtze River’s exuberance. The research thought on the Yangtze River water environment at three stratifications, namely basic research, applied research and aim research, is represented? on the basis of the sub-healthy situation of the Yangtze River,? the view-point of multidisciplinary synthesis and the theory of mountain-river-lake-sea affiliation from the evolution of the river basin system. The emphases are to discuss about the research contents and approaches of some critical problems including the interactive mechanism of mountain-river-lake-sea, rule of the water environment ?evolution, formation of big water environment problems, carrying capacity and controlling elements of the water environment under the effect of human activities and global change. This article aim is to cause people’s attention to the Yangtze River water environment to impulse the research and help constitute the stratagem of new-time river management.