Watershed ecosystem health assessment is associated with ecosystem health. As a new concept, watershed ecosystem healthassessment is an important decision-making basis of ecological protection, watershed management and water resources development andutilization. Meanwhile, it is an important measure. In this study, we established the ecosystem health assessment indices and correspondingthreshold for the Shiyanghe River Basin, and decided the weight of assessment indices by combination weight algorithm, then generatedmodified evaluation approach by set pair analysis. The quantitative assessment results show that the ecosystem health statuses over theupper, middle and lower reaches of the Shiyanghe River are respectively healthy, sub-healthy and unhealthy.