Objective To improve the pathogen detection rate through project-based management mode. Methods Hospitalized patients who received therapeutic antimicrobial treatment in a tertiary first-class hospital from January to December 2022 were selected as the research subjects. The control group comprised patients from January to June, while the intervention group consisted of patients from July to December. The intervention group adopted a project-based management mode with five stages, including project initiation, planning, execution, monitoring, and closure. The monitoring indicators related to pathogen detection were compared between the two groups of patients before and after the intervention. Results A total of 35 488 hospitalized patients received therapeutic antimicrobial agents were investigated, with 15 536 patients in the control group and 19 952 in the intervention group. Pathogen detection rate in the intervention group was higher than that in the control group (69.52% vs 44.10%), with a statistically significant difference (P < 0.001). The goal achievement rate was 430.85%, and the improvement rate was 57.64%. There were statistically significant differences (all P < 0.05) between the two groups of patients in terms of the pathogen detection rate before antimicrobial use, antimicrobial use rate, antimicrobial use intensity, and the detection rate of multidrug-resistant organisms (except carbapenem-resistant Enterobacteriaceae and methicillin-resistant Staphylococcus aureus). The detection rate of relevant biomarkers increased after intervention (53.61% vs 25.01%), with a growth rate of 114.35%, higher than the growth rates of microbial culture, microscopy examination, immunological detection, and other detection items. Among the 87 cases underwent procalcitonin (PCT)/interleukin-6 (IL)-6 detection after the intervention, 17.24% were detected >3 days before therapeutic antimicrobial use. Among the 68 cases underwent microbial culture after the intervention, 20.59% were detected >3 days before therapeutic antimicrobial use. Conclusion The application of a project-based management mode can improve the pathogen detection rate in hospitalized patients. However, attention should be paid to the quality management of pathogen detection.