Iran has performed Health Transformation Plan (HTP) from 2014 to obtain its defined goals. This study assesses and compares university and non-university hospitals' efficiency and productivity in Kerman provinces, Iran. The data of 19 selected hospitals, two years before and two years after Health Transformation Plan, was collected in this cross-sectional study. These data included the variables of physician and nurse number, and active beds as inputs and bed occupancy rate and inpatient admission adjusted with the length of stay as outputs. Data Envelopment Analysis method used to measure hospital efficiency. Malmquist Productivity Index is used to measure the efficiency change model before and after the plan. The efficiency and effect of the plan on hospitals' efficiency and productivity were assessed using R software. The results indicated that all hospitals' average efficiency before the HTP was 0.843 and after the HTP was increased to 0.874. However, it was not significant (P>0.05). Productivity also had a decreasing trend. Based on the DEA method results, it was found that university and non-university hospitals' efficiency and productivity did not increase significantly after the HTP. Therefore, it is recommended that attention be paid to hospitals' performance indicators regarding how resources are allocated and decisions made.