Abstract: The ecological environmental problems of the Yangtze River follow the rules of "symptoms in the water, lesions on the shore and root causes in the structure". The upstream areas mainly face the problem of developing in protection, the midstream areas face the problem of protecting in development, while the downstream areas need to open up a new level of mutual benefit between protection and development. The joint research on the protection and restoration of the eco-environment of the Yangtze River is an innovative model for Ministry of Ecology and Environment and China Three Gorges Corporation (CTG) to carry out strategic cooperation and innovation between the ministry and enterprises. The 14th Five-Year Plan to carry out joint scientific and technological research on the protection of the Yangtze River requires in-depth research on the relationship between environment and economic development, the relationship between major projects and Great Protection of the Yangtze River, and the relationship between pollution prevention systems and ecological management. It is necessary to focus on the three major pollution sources of industry, agriculture and cities, strive to overcome difficulties and pass through the barriers, to accomplish the supporting role of science and technology, so as to better protect the Yangtze River.