The Yangtze River is the largest river in China. It is a priority conservation area for biodiversity of the world, with its main river, branches and wetlands. As an essential part of freshwater ecosystem, aquatic vegetation has been well studied by Chinese researchers since 1950s, but large-scaled analysis on the biodiversity pattern is lacked. Based on published studies, we analyzed spatial and temporal pattern of aquatic plant diversity in the Yangtze River Basin, and calculated the suitable habitat area and underlying influence of environmental factors using MaxEnt software. A total of 298 species are recognized, belonging to 121 genera in 52 families, which is 57.6% of the total aquatic vascular plants in China. The Yangtze River Basin is the key area for aquatic plant diversity of China, especially the subregions of middle reaches. The elevation and land use are the key environmental variables to the spatial pattern of aquatic plants. The separation among water systems have weak influence on the spatial pattern of diversity in aquatic vascular plants, but potamo-lacustrine habitats facilitated the species homogenization of the flora in a sub-basin scale. The network consists of Poyang Lake, Dongting Lake, Tai Lake, and the middle and lower mainstream is the suitable area for the aquatic plants based on the MaxEnt model. In the past half century, the decline or loss of aquatic vegetation occurred in plenty of lakes in the Yangtze River Basin. We suggested that the protection of aquatic vegetation should be incorporated into the integrated conservation of the middle and lower Yangtze River.