Objective To analyze the application effect of the payment of disease type and the payment of single disease payment under the control of total amount. Methods A retrospective analysis of the basic hospitalization expenses, medical insurance fund expenditures and medical insurance fund income under the control of the total value of the disease and the single-income payment model under the total control from 2015 to 2018 were taken, and to have comparative analysis of the total control of the single disease overall operational efficiency of the payment model with the payment model. Results There was a slight fluctuation in the payment of disease value under the control of total amount from 2015 to 2018, but there was no obvious increase, which was stable at around 9 000 yuan, and the balance of medical insurance fund paid for the disease value under the total control was at 17% level and has both stable medical insurance fund expenditure and medical insurance fund income level. Compared with the total score control under the total amount control, the average hospitalization cost under the single disease payment mode was higher, and showed a trend of increasing year by year; compared with the average hospitalization cost in 2015, the average hospitalization cost in 2018 was higher, out of 500 yuan. From 2015 to 2018, the balance of the medical insurance fund paid for the control of the single disease had a large fluctuation, indicating that the medical insurance fund expenditure and the medical insurance fund income level were unstable. Conclusion The disease-based payment model under total control has obvious control effect of medical expenses and medical insurance fund expenses, but it also has a large basic input level and high management cost and other defects. The payment model has the advantage of convenient management, but it is not as good as the cost control and disease coverage, and the single disease payment and the disease value payment under the total control have their own advantages and disadvantages, which need to be based on the regional situation. We need to make use of the strengths and weaknesses, adapt to local conditions and choose the best, to ensure a sound medical insurance payment method.