Retrospective analysis was carried out to select the cases and 10 sample diseases from November 2015 to December 2021 in a grade A tertiary hospital in Nanjing. This paper discussed the effect of the single disease payment method based on the investigation of the overall hospitalization expenses and disease expenses before and after the implementation of the method to explore the effectiveness and provide suggestions for improving the reform of the single disease payment method and the medical insurance payment method. The results showed that after the implementation of single disease payment，the total medical expenses decreased， and overall fund and individual payment have increased. In term of cost composition，drug and anesthesia costs increased，while project and material costs decreased. All results were of statistical significance(P＜0.05). The single disease payment system slowed down the growth of medical expenses to a certain extent，but it has limited effect on reducing patients’personal burden. We should strengthen the control of single disease expenses，actively explore the transition from payment by single disease to Diagnosis ?Related Groups(DRG)， and improve the payment system in which multiple payment methods coexist.