Abstract: The main problem of Yangtze River's ecological environment is the uncoordinated phenomenon between harnessing, development and eco-protection, and heavily exploitation than protection. This paper summarized the achievements of harnessing and development, analyzed the main water safety problems, and provided the coordinated ideas of the harnessing and development and eco-protection of Yangtze River. The main strategies for harnessing and development and eco-protection of Yangtze River in future are put forward, including further strengthening the construction of flood control system and improving the capacity of flood control security, implementing the ecological elements regulation and spatial control and restoring damaged freshwater ecosystem; strictly controlling the pollution load into the rivers and lakes and improving water quality; scientifically regulating the relationship between Yangtze River and Dongting Lake, Poyang Lake. This paper attempts to provide scientific and technological support for harness, development and protection of Yangtze River.