Objective To study and establish the automatic resident prescription system and automatic dispensing system in Center Drug Store based on NO.1 Military Project. Methods According to the Prescription Administrative Policy (2007, Chinese Ministry of Health), automatic system was designed to link each drug store of different departments to the center drug store. Results It is proved that the design is appropriate according to the application of this system in many military hospitals. Conclusion The system not only gives a good administration of drug, but also decreases the work load and increase work efficiency of center drug store.