As the crucially ecological space in a watershed, the waterfront of great rivers shows the unified integrity in the spatial patterns, objectives and ecological functions. This paper provided an in-depth analysis of the scientific connotation of the ecological integrity of the riverfront in terms of the authenticity of shorelines, the ecological gradient on the water-land surface, habitat dependency, and biodiversity. The characterization system of the ecological integrity in great rivers' waterfront was established based on the domestic and overseas literature, and the index system and comprehensive classification methods were proposed correspondingly. Then the ecological integrity of the Yangtze River riverfront was evaluated. The results showed that the ecological integrity of the Yangtze River riverfront was generally at an intermediate level, with the ecological integrity index of the riparian zone gradually decreasing from the upstream to the downstream. The riverfront of the cities in the middle and upper reaches was affected by the growth conditions of riverside wetlands and islands as well as the preservation of wetlands. In contrast, the riverfront of the downstream cities was constrained by the intensity of land development, the proportion of natural waterfront, and the connectivity of water and land. Although the ecological integrity of the middle and lower reaches of the riverfront has been significantly affected by the social development and the barrier of the Yangtze River dam, there was still spatial heterogeneity in ecological integrity under the same conditions, with some areas still maintaining high levels of integrity such as Tongling, Anqing and Shanghai sections. The assessment of the riverfront ecological integrity will help to promote the formation of the natural waterfront pattern of the Yangtze River that not only respects the nature, protects the ecological environment, ensures flood control and water supply safety but also supports social and economic development and efficient and intensive utilization.