The evaluation system of watershed ecosystem is the basis for evaluating the health of the watershed, and the evaluation results provide the basis for the protection measures and policy making of the watershed ecosystem. In the premise of introducing watershed ecosystem health, this paper summarized the development history and current situation of the ecological system assessment theory and evaluation indicator at home and abroad, integratedthe popular evaluation systems, and discussedthe five kinds of practical models includingthe water -based system evaluation model, the improved matter -element analysis, the biological integrity index method, the model of pressure state response (PSR) and the landscape pattern analysis. It is essential to select appropriate assessment system for evaluating the health status of the watershed ecosystem. The comprehensive index evaluation system, including the 5 indicators of physical environment, biological environment, social environment, ecological function and social function, was obtained to evaluate the watershed system. The paper also made prospects according the existing problems of the evaluation system.