Abstract:According to the requirements of cost accounting，drug circulation should follow the rule of first-in first-out. At the same time，price adjustment should not appear in the report. While the existing drug management system can not meet the requirements mentioned above，making the report do not satisfy the cost accounting specification. In order to achieve the goals，it is necessary for batch managements of drugs in the drug information system and making income statement change to the cost statement. Taking the dual characteristics of drug into consideration，which are materials and medical care，combined with the actual situation of hospital，we want to conduct a comprehensive transformation of the drug information management system of the HIS system and complete the drug batch management from the drugstore to pharmacy to patients. Aims to reduce medical disputes from drug management and use and make the drug management be more scientific，standard and specification to provide scientific decision basis for hospital management. This article focuses on process and program implementation of drug batch management in pharmacy storage and pharmacy ,and concerns about the generation and consumption of batches in pharmaceutical inventory. It emphasizes the scientific management，convenient operation and data accuracy. Some problems in the process of implementation are also discussed and analyzed in this paper.