Abstract: Based on the actual needs of ecological environmental protection and restoration of the Yangtze River, theoretical thought on synergistic management of the ecological environment of the Yangtze River from multiple dimensions was carried out, the practical experience of National Joint Research Center for Yangtze River Conservation (NCYC) in the past two years was summarized, and suggestions on the further synergistic management of the ecological environment of the Yangtze River was put forward. The results showed that: 1) The synergistic management of the ecological environment of the Yangtze River has four core connotations, namely, synergy of governance subjects, governance objectives, treatment measures and performance evaluation. Its purpose is to realize the maximization of governance effectiveness and maintain the public interest of the ecological environment to the greatest extent. 2) Strengthening the synergistic management of the ecological environment of the Yangtze River is of great significance. It is an important measure to implement the spirit of General Secretary Xi Jinping’s important speeches on promoting the development of the Yangtze River Economic Belt, an inherent requirement for modernizing the ecological environmental governance system and capacity of the Yangtze River, and an inevitable choice for promoting the fundamental improvement of the ecological environmental quality of the Yangtze River and building a beautiful Yangtze River. 3) NCYC had innovatively constructed the synergistic model of the joint research for the Yangtze River ecological environmental conservation based on the coupling architecture of “Umbrella-shaped” and “Fan-shaped” models. And a joint research service mechanism had been established through joint tackling of key problems and technological assistance for cities contracted by different research teams. With scientific and technological synergistic innovation as the core, the system interaction of “the five systems” was promoted, including expert resources, information knowledge, governance subjects, governance objectives and measures, and examination and estimation of the Yangtze River protection and conservation. The orderly synergy of the “the six aspects” was realized, including data resources, intelligence knowledge, responsibility, examination and estimation, quality control of method, and joint prevention and control. Then, it helped the national and local governments achieve practical results in implementing scientific and precise pollution control, maximized the overall effectiveness of the think tank of scientific and technological talents, and promoted the improvement of the Yangtze River ecological environmental synergistic management capacity. 4) It was suggested that in the future, the institution and mechanism of scientific and technological synergistic innovation in joint research should continue to be improved and popularized, the theoretical research and practical exploration related to synergistic management of the Yangtze River ecological environment continue to be deepened, and the construction of the performance evaluation mechanism of synergistic management of the Yangtze River ecological environment be accelerated.