Objective Our study aims to enhance the precision of internal control construction within public hospital supply chains and minimize the subjective bias influence. We have integrated the game theory combination weighting method into the design of internal control paths and based on this, developed a series of pioneering solutions. This innovative approach is anticipated to heighten the effectiveness and scientific rigor of the internal control design scheme within the supply chain. Method Firstly, we utilized literature review and expert interviews to delve into the key factors of public hospital supply chain internal control, forming an index system for public hospital supply chain internal control that aligns with current informatization requirements. Subsequently, we incorporated the Game Theory Combination Weighting Method into this study. By means of the Analytic Hierarchy Process and the Entropy Weighting Method we determined the subjective and objective weights of each index and obtained their comprehensive weights through the Game Theory Combination Weighting Method. Then, based on the analysis results, we designed a series of internal control construction schemes and implemented these schemes at Weifang Maternal and Child Health Hospital between 2019 and 2023. Finally, using the Fuzzy Comprehensive Evaluation Method to assess and compare the actual effects before and after the implementation of the schemes, thereby validating the effectiveness of the Game Theory Combination Weighting Method in the design of the internal control path of public hospital supply chains. Results The fuzzy comprehensive evaluation results for the years 2019 and 2023 demonstrated that after implementing our design schemes using the Game Theory Combination Weighting Method, the hospital’s satisfaction in aspects such as plan-side control, purchase-side control, asset-side control, expenditure business control, and contract management control has significantly improved. Conclusion Our research indicates that the Game Theory Combination Weighting Method is applicable to the path design of internal control links in public hospital supply chains. This method has effectively enhanced the targeted improvement of weak links within the construction of internal controls in the supply chain of public hospitals and is of great significance for improving the scientific nature of supply chain internal control management.