Maintaining a healthy state of rivers is the basis for their functions, and the scientific evaluation of river health has significant implications for the environment, ecology, and socio-economics. In this study, the practical needs of river management and the need to establish a new type of human-water relationship were considered, resulting in the construction of a river health evaluation indicator system with 13 indicators based on the criteria of hydrology and water quality, habitat structure, aquatic organisms, social services, and river management. Additionally, a comprehensive index of river health assessments was proposed to judge the health level of the river. The comprehensive river health evaluation indicator system was applied to the Taihu Lake Basin, and the results indicated that the evaluation indicator system could objectively and scientifically reflect the health level of the river. The comprehensive index of river health assessment was calculated to be 73.38, indicating that the overall health of the river was in a “healthy” state. However, further improvements were needed in areas such as river connectivity. The study presents a new evaluation system and methodology that facilitate the development of effective strategies for river conservation and management.