Objective: To analyze the variation in the medical expense structure of public hospitals in Anhui and Zhejiang provinces from 2012 to 2021, providing references for establishing a rational medical cost control mechanism and for informing medical policy reform. Method: Descriptive and structural variation analysis methods were used to compare the medical expense data of public hospitals in Anhui and Zhejiang provinces from 2012 to 2021. Results: During the sampled period, the increase in medical expenses in Anhui and Zhejiang provinces aligned with the local economic development trends, indicating a positive status in the development of the healthcare sector in both provinces. Conclusion: In Anhui and Zhejiang provinces, public hospitals have achieved some success in controlling medical costs, but there is still room for reducing the proportion of drug expenses. In comparison, Zhejiang Province's public hospitals have been more effective in controlling medical service costs. However, the control of outpatient costs is less satisfactory when compared to inpatient costs.