OBJECTIVE： To explore new method of prescription comment in medical institutions of Chongqing under the background of “New Medical Reform”， and to provide reference for prescription comment innovation and promoting rational drug use in clinic. METHODS： Through analyzing policy background of prescription comment innovation and practice， referring to experience of other regions， the achievements and problems were analyzed by developing centralized prescription comment and prescription comment information construction in municipal and regional （county-level） medical institutions of Chongqing. The countermeasures suggestion was put forward. RESULTS&CONCLUSIONS： The prescriptions of 16 municipal medical institutions were commented centrally， involving more than 300 medical records and 1 600 prescriptions or medical orders. The prescriptions of 135 regional （county-level） medical institutions were commented centrally， involving more than 3 100 medical records and 12 100 prescriptions or medical orders. “Chongqing Medical Institution Prescription Comment Key Technology Monitoring System” was established. Above measures innovated centralized prescription comment mode， improved the quality of prescription comment and promoted prescription comment informatization. There were still problems as incomplete coverage of the system， inspection to become a mere formality. It is suggested to strengthen internal quality control of medical institutions by establishing rational drug use scoring management system， developing clinical pharmacist ward round and prescription checking in advance； establish and improve third-party external comment and supervision mechanism； improve the knowledge of prescriptions comment staff in all directions so as to further standardize prescriptions and promote rational drug use in medical institutions.