Abstract: objective: To analyze the input-output efficiency of 8 sample tertiary hospitals in 2011-2016, and put forward reasonable suggestions for the improvement of scientific research efficiency in tertiary hospitals.Methods: Using the method of factor analysis to screen the input and output indexes of the related scientific research, and to study the input-output efficiency of tertiary hospitals through DEA. Results: The efficiency of scientific research in eight tertiary hospitals was effective in the period of 2011-2016. The efficiency of scientific research in the comprehensive hospital was higher than that of the specialized hospitals. In terms of scientific research management ability, the tertiary hospital has steadily improved, but still is still below the general hospital. In the field of scientific research resource allocation, the main problem of general hospital is to devote resources to redundancy, while specialized hospitals are mainly devoted to insufficient resources.Conclusion: Government and hospital research management departments should try to build different types of hospitals and research exchange platforms between colleges and universities to improve the efficiency of total research input and output of tertiary hospitals. By improving the scientific research management mechanism and personnel training mechanism of specialized hospitals, we can realize the development of scientific research innovation, and further improve the scientific and diversity of hospital research funds allocation.