Objective: In order to cope with the rising risk pressure on the economic operation of public hospitals, it aims to re- search and construct a comprehensive economic operation evaluation index, and improve the comprehensiveness, scientific and dynamic nature of monitoring and analysis of the economic operation of public hospitals. Methods: Literature research, expert consultation and hierarchical analysis were adopted. Results: A comprehensive evaluation model of public hospitals’economic operation covering 5 dimensions and 25 indexes, including structural optimization, controllable risk, efficiency enhancement, smooth operation and sustain- able development, has been constructed; empirical analyses of the overall index, sub-indexes and monthly indexes have been carried out on the data of some of the tertiary hospitals in Shanghai, which have verified the validity of the above index model in enhancing the monitoring, analysis and evaluation of the hospitals’economic operation, and revealed the role of the above index model in the changes of the economic conditions of the hospitals and the factors. Conclusion: Constructing a comprehensive evaluation index can effectively complement management such as comprehensive assessment and evaluation of public hospitals and traditional financial descriptive analysis.