Objective To investigate the effectiveness of continuous improvement projects based on FOCUS-PDCA on the pathogen sample submission rate before antimicrobial therapy for inpatients. Methods FOCUS-PDCA was used to improve the pathogen sample submission rate in Affiliated Hospital of Nantong University from Jun. to Jul. 2023. The inpatients from Jan. to May 2023 (before improvement) were enrolled as control group, and the inpatients from Aug. to Dec. 2023 (after improvement) were enrolled as improvement group. The utilization rate of antibiotics, the submission rate of pathogen samples, the submission rate of clinical microbial samples and the detection rate of multidrug-resistant organisms were compared between the 2 groups. Results The utilization rate of therapeutic antimicrobial agents (32.18% vs 32.93%, P＝0.003) and antimicrobial consumption intensity (39.99 defined daily dose ［DDD］/100 patient-days vs 44.19 DDD/100 patient-days) in the improvement group were significantly lower than those in the control group. The pathogen sample submission rates before antimicrobial therapy and key antimicrobial combination therapy in the improvement group were significantly higher than those in the control group (52.01% vs 23.64%, 87.74% vs 77.71%; both P＜0.001). The qualified rate of microbial specimens in the improvement group was significantly higher than that in the control group (88.77% vs 80.11%, P＜0.001). The detection rates of multidrug-resistant organisms and carbapenem-resistant Klebella pneumoniae in the improvement group were significantly lower than those in the control group (40.45% vs 48.42%, 29.65% vs 43.17%; both P＜0.001). Conclusion The continuous improvement projects based on FOCUS-PDCA can improve the pathogen sample submission rate, reduce the detection rate of multidrug-resistant organisms, and promote standardized hospital infection quality management.