Objective: To compare the differences in the total per-average inpatient costs of traditional Chinese Medicine (TCM) dominant diseases treated in TCM hospitals and general hospitals, and to explore the cost characteristics of 213 inpatient dominant diseases treated in different types of medical institutions. Methods: The data of this study were selected from the information on TCM dominant diseases inpatients discharged from 58 hospitals in Beijing from January 1, 2016, to December 31, 2019, and the propensity score matching method was used to eliminate confounding from the extracted basic data of inpatients. Results: Data were collected from 605 688 inpatients with TCM dominant diseases, and the results showed that the overall average total cost of secondary hospitalization for dominant diseases in TCM was higher in general hospitals than in TCM hospitals, and the cost structure of dominant diseases in TCM hospitals reflected the characteristics of TCM treatment. Conclusion: It is needed to actively promote the payment by disease for the advantageous diseases of TCM, fully consider the characteristics of each disease, and focus the cost structure adjustment on the adjustment of medical behavior and the advantage of TCM.