[Objective] Taking Dongyang River basin as the research area, to carry out watershed ecosystem health assessment, in order to provide conferences for decision-makings of ecological comensation system in this region.[Methods] According to technical guidelines of watershed ecosystem health assessment issued by Ministry of Environmental Protection, we set 6 evaluation categories, 17 indexes to assess the ecosystem health of 29 units in Dongyang River basin. The evaluation categories included water habitat structure, aquatic organisms, water ecological pressure, land ecological pattern, land ecological function and land ecological pressure.[Results] The project had completed the ecosystem health assessment of 29 units in Dongyang River basin. The evaluation results showed that:The ecosystem health of Dongyang River basin can be classified as excellent, good and general, accounting for 6%, 60% and 34% of the total area, respectively. The main limiting factor of aquatic ecosystems was water quality index, while land ecological limiting factors were mainly the forest coverage rate, the proportion of construction land, important habitat retention and water conservation functions. Ecosystem health was at a higher level in hilly area, and found at a lower level in plains and basins; and meanwhile, the upper stream ecosystem health level was higher, while densely-populated middle and lower reaches were at lower level.[Conclusion] It was the types and intensity of human activities that led to the regional difference of ecosystem health in Dongyang River basin. The most serious ecological environment problems in the basin listed:the poor water quality in the main stream, highly occupied proportion of construction land, point and surface sources of pollution.