Abstract: The research on water ecology of drainage basins has gradually changed from the traditional single evaluation of water quality to the assessment of ecological quality of the rivers. The ecological conservation and development of river basins, based on river health security, has become an international trend. In China, the ecological conservation and development in the Yangtze and Yellow River basins are major national strategies. This research targets the Yangtze and Yellow River basins, and summarizes their aquatic ecological environments. On a basis of the concept that the core of the basin management is to focus on the integrity of the basin, it analyzes the research works that are available to maintain the aquatic ecological health of the two basins. Finally, the landscape-value-oriented strategy of ecological protection is put forward taking into consideration of ecological restoration and landscape design.