Abstract: Wetland is one of the three ecological systems on earth, and it is also the most closely related with human production and life. From West to east, the Yangtze River flows through three steps geomorphology and many climatic zones in our country, wetland types and biodiversity are rich. However, the rapid economic and social development have also brought great challenges to the protection of the Yangtze River Wetland. In this paper, the characteristics of water cycle and the relationship between water cycle and habitats of typical natural wetlands such as the Yangtze plateau swamp, plateau lake, the lakes that connecting the Yangtze River, middle and lower stream beach and estuarine coast were separately discussed, to provide reference for the protection of the Yangtze River Wetland. The analysis shows that the vertical water cycle of the Yangtze Plateau, the horizontal water cycle of the lakes and rivers in the middle and lower reaches, and the tide of the Yangtze estuary are the key hydrological factors to maintain the ecological function of the wetland respectively. Climate change and human activities are the main factors affecting wetland water cycle and ecological function, plateau wetland and estuary of the Yangtze River are more significantly affected by climate change. The basic principle of wetland protection should be to maintain its natural water cycle as far as possible, and the best plan is to take adaptive measures of protection and management.