Objective To evaluate the management and indicators of pathogen detection before antimicrobial treatment for inpatients in second level and above medical institutions (MIs) in Guangdong Province, and provide direction and decision-making basis for the improvement of pathogen detection quality in the region. Methods The ma-nagement status, information system functions, and pathogen detection rate indicators of secondary and above MIs in 21 cities in Guangdong Province was surveyed through online questionnaire surveys and system submission. A baseline survey on sentinel monitoring MIs was conducted from July 15th to August 8th, 2023. From November 7th to 30th, a baseline survey on non-sentinel monitoring MIs was launched. Surveys on indicator information of all MIs were completed from January 15th to 30th, 2024. Results A total of 265 MIs were surveyed, and the proportions of establishing special working groups (83.98%), developing special action improvement plans (79.01%), establishing pathogen detection rate management systems (91.71%), and developing management assessment plans (76.80%) of tertiary MIs were all higher than that of secondary MIs, differences were all statistically significant (all P<0.05). The proportion of tertiary MIs with various information system functions was higher than that of secondary MIs (all P<0.05). The pathogen detection rate (61.07%) before antimicrobial treatment and healthcare-associated infection (HAI) diagnosis-related pathogen detection rate (88.00%) of inpatients in tertiary MIs were both higher than those in secondary MIs (both P<0.05). Among different types of MIs, pathogen detection rate before antimicrobial treatment of inpatients in maternal and child health MIs was higher than that in other types of MIs. HAI diagnosis-related pathogen detection rate in other specialized hospitals was the highest, and pathogen detection rate before combined use of key antimicrobial treatment in traditional Chinese medicine hospitals was the lowest, differences were all statistically significant (all P<0.05). Conclusion Tertiary MIs have more advantages in management strategies and information technology construction than secondary MIs, secondary MIs need more guidance and support. Monitoring and analysis of pathogen detection rate indicators in MIs of different levels and types should be strengthened through special actions.