Abstract:The current methods of ecological risk assessment (ERA) are difficult to be applied on ecosystem level, since they mainly focus on specific materials or species. An ecosystem-based river ERA method was developed depending on the concepts of system ecology and complex system theory. Distinguishingly, the method selected “Ecosystem Services” as assessment endpoints, and quantified “Pressure-Response” relationship between external stress on ecosystem and Ecosystem Services. Yellow River in China was chose as a case study. The results suggest that the most risky area of Yellow River ecosystem were middle and lower reaches; the main risk sources were urban and agriculture; and the most dangerous targets were habitats and biota. By its application in Yellow River, this method was showed to strongly support ecosystem-based river management.