Yangtze River is a large river system and is rich in biodiversity. Its health status not only affects the sustainable development of the basin economy and society, but also receives wide concerns from both China and abroad. In this paper, the theories and practices of river health assessment in China and abroad are reviewed, and on this basis, the methods and standards of river health assessment suitable for the Yangtze River are discussed. The change of water environment and water ecology of the Yangtze River in the recent decade are analyzed in terms of two indexes: standard-reaching rate of water functional zone, and fish diversity. Last but not the least, the health progress of the Yangtze River after a series of great protection actions in recent years is summarized. The health assessment of the Yangtze River can be divided into different spatial and temporal scales according to management needs. Single index assessment or multi-index comprehensive assessment can be performed according to the integrity of data. The water quality of the Yangtze River has been improved continuously; the water quality in lakes and reservoirs and the biodiversity in rivers and lakes have begun to stabilize; the excessive disturbance on rivers and lakes by human beings has been restrained. Nevertheless, the improvement of water quality in lakes and reservoirs and the restoration of biodiversity still need to be carried out for a long time.