Purpose In order to evaluate the effect of The Public Hospital Reform Policy (PHRP) implemented by Jilin Province in 2017 on improving the operational efficiency of public grade III level A hospitals (3A hospitals) and analyse the items in the policy that play a significant role in improving the efficiency of 3A hospitals, this research analyses whether the PHRP implemented can achieve the expected effect and help 3A hospitals improve their operations. Materials and methods The data comes from the annual health financial summary system of the Health Commission of Jilin Province.The Data envelopment analysis (DEA) was used to analyse the operational efficiency of 3A hospitals. The Malmquist index was used to support DEA findings. Tobit regression was used to analyse the impact of various reform projects in the PHRP on the operational efficiency of 3A hospitals. Results The PHRP has played a positive role in the operational efficiency of 3A hospitals. After the implementation of the PHRP, the average size efficiency score increased to 0.934, the average technical efficiency score increased by 0.063 and the average overall efficiency score improved by 0.086 of the twenty-two 3A hospitals. However, the effect is limited. Controlling the proportion of drug revenues in 3A hospitals is significantly helpful to the improvement of their operational efficiency, but the rise of patients’ treatment expenses has not been effectively controlled. Conclusions PHRP has had a positive effect on controlling drug revenues in 3A hospitals and the next step in the policy should be to find ways to reduce treatment costs to further improve efficiency in 3A hospitals.