Objective By using Data Envelopment Analysis to evaluate comprehensive public hospitals with different levels in Jiangsu Province, its aimed to give scientific suggestions for promoting medical resources rational allocation. Methods With Data Envelopment Analysis, technical efficiency, pure technical efficiency and scale efficiency can be calculated. The emphasis of the analysis is comparing the differences of the efficiency of the comprehensive public hospitals. Tobit regression is applied to analyze the influencing factors. Results Grade 1 and Grade 2 hospitals are inefficient and the results indicate that efficiency of the two different kinds of the hospitals varies in different regions. However, Grade 3 hospitals are efficient comparatively. Conclusion The result of the research can be used to reallocate resources and optimize the scale of the hospitals to improve efficiency of comprehensive hospitals with different levels.