Abstract: In recent years, many university hospitals around the world have gradually explored the establishment of evaluation indictor system including medicine, teaching, scientific research and so on, and have established corresponding evaluation criteria. But for the indictor systems, there are few comprehensive evaluation indictor systems that contain the combination of quantitative and qualitative indexes for medicine, teaching and scientific research. They also lack the evaluation mechanism for rolling out the unqualified hospitals in the process of development. In this study, according to the actual situation of the affiliated hospitals at Capital Medical University, and through literature review and expert consultation method, we initially established a university hospital evaluation index system with both qualitative and quantitative indexes. We have applied the system to evaluate four hospitals, and improved the medical treatment, teaching and scientific research levels of our university hospitals. The research also has important practical significance to promote the medical education and enhance the comprehensive strength of the university hospitals.