Objective To establish an evaluation system of pathogen detection rate of hospitalized patients before antimicrobial treatment based on process and outcome indicators, and study its application effect. Methods Hospitalized patients with therapeutic antimicrobial treatment in a tertiary first-class hospital from July 2022 to June 2023 were selected as the study objects. Difference in process and outcome indicators were compared between before (July-December 2022, control group) and after (January-June 2023, intervention group) the implementation of intervention in the evaluation system for pathogen detection rate of hospitalized patients before antimicrobial treatment. Results 41 577 and 27 052 hospitalized patients received therapeutic antimicrobial agents were included in the intervention group and control group, respectively. Pathogen detection rate and the accurate pathogen detection rate in the intervention group were both higher than those in the control group (74.2% vs 62.8% and 90.3% vs 82.5%, respectively), both with statistically significant differences (both P < 0.001). The goal achievement rate and improvement rate for pathogen detection rate were 237.5% and 18.2% respectively, the goal achievement rate and improvement rate for accurate pathogen detection rate were 104.0% and 9.5% respectively. For the process indicators, the conformity rate of detection and diagnosis, accurate collection rate, timely transfer rate, acceptance rate of pathogen specimens in the intervention group were all higher than those in the control group, differences were all statistically significant (all P < 0.001). For the outcome indicators, detection rates of targeted indicators and blood culture specimens, pathogen detection rate before treatment of restricted and special grade antimicrobial agent, as well as detection rate of sterile body fluid specimens in the intervention group were all higher than those in the control group, with statistical significance (all P < 0.05). In addition, the positive rate of blood culture specimens increased from 18.5% before intervention to 21.7% after intervention, with statistically significant difference (P < 0.05). Conclusion The establishment of indicator evaluation system can improve the detection rate and accurate detection rate of pathogens before antimicrobial treatment, as well as the management quality and connotation of indicators.