With the continuous deepening of public hospital reform and implementation of internal control systems in China, comprehensive evaluation of the implementation effect of internal control systems in public hospitals is gaining greater weight. To explore the comprehensive evaluation method for such aspect, the authors selected 31 indexes in 6 dimensions based on the analysis of evaluation indexes to construct a comprehensive evaluation index system. The Delphi method was used to determine the relative weight of each evaluation index, and a fuzzy comprehensive evaluation model for the implementation effect of the internal control system in public hospitals was constructed. This paper conducted an application study on the comprehensive evaluation of the implementation effect of the internal control system in a hospital in Suzhou to verify the effectiveness of the model, and a comprehensive evaluation of the implementation effect of the internal control system in the public hospital was implemented. These efforts provided an effective management method for analysis of the implementation effect of the internal control system in public hospitals.