Objective To develop a precise diagnosis and treatment system for pulmonary and critical care medicine, explore the value of the system in promoting the rational antimicrobial use, and promote the rational use of antimicrobial agents from the source. Methods Patients discharged from the department of pulmonary and critical care medicine of Xiangya Hospital of Central South University from 2012 to 2021 were taken as the research objects. Antimicrobial stewardship (AMS) was integrated into the precise diagnosis and treatment system for pulmonary and critical care medicine, and antimicrobial use before and after the implementation of the system were compared. Results A total of 2 947 discharged patients were included, 1 105 of whom were pre-implementation cases and 1 842 were post-implementation cases. Among the discharged diagnosis, 2 643 were infection cases (89.7%), including 963 pre-implementation cases (87.1%) and 1 680 post-implementation cases (91.2%). Despite an increase in the proportion of infected cases after implementation, antimicrobial use decreased by 2.9% compared to before implementation cases (97.0% vs 94.2%, P < 0.001). Compared to the pre-implementation period, the intensity of antimicrobial use decreased by 12.4% (244.4 DDDs vs 214.1 DDDs) and the intensity of special-use antimicrobial agents decreased by 14.4% (131.0 DDDs vs 112.2 DDDs), both shifting from high fluctuations to linear declines (P < 0.001). Conclusion The precise diagnosis and treatment system for pulmonary and critical care medicine effectively promotes the rational and precise use of antimicrobial agents, with the clinical treatment team as the core of the system, and emerging diagnostic and treatment technologies playing an important role.