Objective:To evaluate the relative efficiency of pharmacies in military hospitals,so as to provide evidence for rational allocation in medicinals resources in hospitals. Methods:Data envelopment analysis (DEA) was used to evaluate relative efficiencies of 71 pharmacies in military hospitals (also as decision making units,DMUs). The input factors included pharmacy personnels,equipment,areas of pharmacies,and development funds; the output factors included drug charge,clinical pharmaceutical service,pharmaceutical information service,academic achievements and research activities. Decomposition of the pharmacy efficiencies under different economic conditions was performed to evaluate the scale efficiency (SE),the resource disposal efficiency (DE) and the technical efficiency (TE). Pearson correlation analysis and chi-square test were used for statistic analysis. Results:DEA results showed that the relative efficiency of the 28 pharmacies was 1, they were DEA effective; the relative efficiency of the 43 DMUs was less than 1,indicating the presence of efficiency loss. Multiple linear regression analysis showed that hospital grade,bed number,clinical time of pharmacists,HR flow-in rate,proportions of pharmacists with undergraduate or graduate diploma,bed utilization rate,etc. were correlated with the 5 output factors. Five multiple linear regression equation were established. We also found that the distribution of pharmacies of SE,DE,and TE non-efficiency were significantly different between hospitals of different grades; the distribution of pharmacies of DE, and TE non-efficiency were significantly different between hospitals located in different regions. Pearson correlation analysis showed that the DEA efficiency of pharmacies was correlated with hospital grade,not with the area or the city where the hospitals located. Conclusion:The grades of military hospitals and the subsequent effective allocation of resources and technologies may be the key factor to increase the efficiencies of pharmacies.