Abstract: “Scatter degree” method is generally blamed for not capable of reflecting the subjective information of evaluator in comprehensive evaluation and for the complexity, uncertainty, and variety of the factors affecting river ecosystem health. In this paper, the “scatter degree” method was improved and applied to comprehensively evaluate the ecosystem health status of the upstream, midstream, and downstream of Beiyunhe River which flowed through Beijing and Tianjing. The ecosystem health value of upstream, midstream, and downstream was evaluated as 0.539, 0.521 and 0.546, respectively, indicating that these streams were in subhealth condition. The environmental status of flowing water was the most important factor affecting the River’s ecosystem health. With the application of the improved method to evaluate river ecosystem health, both the evaluator’s subjective judgment and the data’s objective information could be included, the evaluation process was transparent, and the evaluation results were scientific, reasonable, objective, and reliable, suggesting that this method could be served as a technical support and a basis for the comprehensive treatment of rivers.