Abstract: The health of ecosystem in the Yangtze River Economic Belt (YREB) is an important key factor to the sustainable development of China’s economy and society. Based on the framework of Vigor-Organization-Resilience Contribution, an ecosystem health assessment model was built for the YREB, and the ecosystem health for each country in 2000 and 2015 was analyzed. The result showed that: (1) The ecosystem health was higher in the upstream and south of the Yangtze River (e.g. Yunnan province), while lower in the downstream and north of the Yangtze River (e.g. Anhui province and Jiangsu province); (2) An overall increase of ecosystem health index was detected from 2000 to 2015. However, in some local areas, especially coastal regions of Yangtze River Delta Area, the ecosystem health index decreased; (3) In 2015, the ecosystem health of the Yangtze River Economic Belt was dominated by four factors, the four-factor dominant area accounted for 41.2% of the total area, and most of them were transformed from the primary three-factor dominant area in 2000. In general, the ecosystem health of the YREB recovered during the study period, but declined in the areas with intensified human activities.