Objective: To study the changes of hospitalization expenses of gallstone patients before and after the comprehensive reform of separation of medicines and medical consumption in Beijing, and evaluate the achievements and existing problems in these two rounds of reforms. Methods: The interrupted time series (ITS) model was applied to analyze the changes of total and detailed hospitalization expenses before and after the two reforms in 111 secondary and tertiary medical institutions in Beijing. Results: After the reforms, the total hospitalization expenses of patients with gallstones in secondary and tertiary medical institutions increased slightly, and the drug and material expense per capita percentages declined, while the medical expense rose. The average medical expenses and material expenses per capita of secondary medical institutions increased after reforms, the average drug expenses of tertiary medical institutions decreased after reforms, while the medical expenses per capita continued to increase. Conclusion: These two rounds of reform have basically achieved the expected policy goals. It is suggested to strengthen the management of medical consumables, optimize the internal and external compensation mechanism of hospitals, promote the construction of the hierarchical medical system, and improve the effectiveness of public hospital reform.