In this paper, we study data mining of the antimicrobial drug based on immune genetic algorithm. The accuracy of traditional approach for data mining is poor. The immune genetic algorithm technology, which is applied to the data mining of antimicrobial drug can improve the accuracy and timeliness of data mining. Data mining provides a new idea for the effective analysis of the relationship between the disease and its occurrence regularities, which helps better curing the disease and improving the treatment effect. By immune genetic algorithm, it analyzes and mines antibacterialdrug data in HIS, and obtains the rules and trends of potential, which gradually establishes the diagnosis knowledge database of antibacterial drug. According to the doctor's order data of HIS system and autonomous learning and updatding the knowledge database, the approach provides a reasonable assistant decision for doctors to treat patients.