Objective To develop and improve the microbiology laboratory information management system (LIMS) in Peking Union Medical College Hospital. Methods According to the requirements of practical operations, the corresponding program was compiled and continuously upgraded to develop a LIMS suitable for the workflow of microbiology laboratory. Results The LIMS for microbiology laboratory possessed five modules: the management for task, identification, quality, statistics and system setting. The hardware facilities, e.g., microscope, photographic imaging system, automatic microbial identification and antimicrobial susceptibility analysis system and blood culture instrument could all be connected with the LIMS to realize data transmission. The record, delivery and paperless office work for every part in the whole process of microbiology laboratory were realized, including receiving, inoculating culturing, antimicrobial susceptibility testing and reporting of specimen, quality control and data statistical analysis. The efficiency of laboratory operations was significantly improved and more labor resources were released. The operators, the operation subjects and time of operation at each link point could be recorded and the supervision for all the operation were realized. The error rate in operations was reduced and the work quality was effectively ensured. Conclusion A set of constantly improved LIMS for microbiology laboratory that meets the needs of the actual operations may clarify the complex manual operation process in laboratory, and the monitoring for whole process and standardized management in microbiology laboratory may realize.