Based on the pressure-state-response(PSR)conceptual model, an assessment index system of river ecosystem health was established for quantitative assessment of the ecosystem health status of the Huangbai River. The analytic hierarchy process was used to determine the index weight. The ecosystem health status of the Huangbai River was evaluated comprehensively using set pair analysis and attribute recognition theory. The results show that the comprehensive ecosystem health status of the Huangbai River was at the medium level, with the health status of the pressure subsystem, the state subsystem, and the response subsystem at a high level, medium level, and high level, respectively. The main factors that affect the ecosystem health of the Huangbai River included the water eutrophication index, pesticide application intensity, and soil erosion rate.