Objective To analyze the impact of canceling drug price markup policy on hospitalization expenses of urban public hospitals in Sichuan province and provide decision-making basis. Methods Data of hospitalization expenses of the top 50 diseases among inpatients discharged in 2016 and 2017 were collected, totaling 2 732 022 inpatient cases. Based on hospitalization expenses, these disease were divided into seven categories ( A-G) using dynamic clustering analysis, which represent respectively dominant diseases of different expense makeups, to compare such indicators as hospitalization expenses and composition ratios of these diseases before (2016) and after the reform (2017). Results The study found drastic changes among the medical expenses of different categories of dominant diseases. For example, per-hospitalization cost of categories E ( featuring high drug and examination expenses ) and G ( featuring balanced expenses distribution) diseases decreased since the reform, while the other categories rose instead. The proportion of drugs of different disease categories decreased to various extents. For example, category A ( high drug ratio of 5.60% ) and category E (5.15% ) diseases of which were found with the sharpest drop. Proportion of service expenses, on the other hand, rose to different extents. For example, the proportion of service expenses of all disease categories increased to varying degrees, among which category E (3.46% ), category F (3.37% ) and category D (3.36% ) accounted for the largest share of increase.Conclusions The reform is moving the cost structure of dominant diseases in Sichuan towards a rational level, yet with significant differences among disease categories. The authorities should target various categories to adjust their reimbursement policies, minimize financial burden on patients, strengthen their supervision on drug use and medical behavior, prevent such misbehaviors as the inducing demands and transferring drug markups.