Jiulong river basin ecosystem was divided into terrestrial, riparian and aquatic ecosystems as the evaluation objects, combined with the natural conditions, socio-economic characteristics and ecological problems, the characteristics of different ecosystems structure were analyzed, function and ecological stress, the index system of watershed eco health assessment of Jiulong river basin were constructed from the viewpoint of ecosystem′s physical, chemical, and biological integrity. Using RS and GIS technologies, the sub-watershed was studied as evaluation unit, a holistic systems approach was taken to assess the health condition of watershed ecosystem. The research indicated that comprehensive index for ecological health condition of Jiulong river basin is in a fair level. The terrestrial eco-health condition is better than eco health condition of riparian ecosystem and aquatic ecosystem. In view of spatial distribution, the upstream source area in Beixi river is in the highest level of health condition, which is better than the middle and lower reaches of Beixi river and Xixi river. Based on the primary intimidation factors of ecosystem health impairment of Jiulong river basin, the management countermeasures are put forward, which of water habitat restoration, riparian comprehensive improvement and terrestrial pollution reduction.