Objective To improve the submission quality of clinical microbial specimens through applying comprehensive intervention measures. Methods Patients who used therapeutic antimicrobial agents in a hospital from September 2018 to August 2020 were investigated, comprehensive intervention measures were implemented from September 2019. Comprehensive intervention measures included signing responsibility agreement, work quality assessment and feedback, knowledge training, and information system control. Submission rates of microbial specimens, sterile specimens, respiratory tract specimens and blood culture specimens of inpatients before (September 2018 to August 2019) and after intervention (September 2019 to August 2020) were compared. Results A total of 40 335 inpatients who used therapeutic antimicrobial agents were investigated, including 21 441 before intervention and 18 894 after intervention. After the intervention, submission rates of microbial specimens before antimicrobial the-rapy, restrictive antimicrobial therapy, and special antimicrobial therapy were 65.20%, 67.36% and 99.02% respectively, which were higher than 63.64%, 64.68% and 91.27% before intervention (all P < 0.05). Submission rate of sterile specimens increased from 13.81% before intervention to 15.85% after intervention, submission rate of respiratory specimens decreased from 37.63% before intervention to 35.68% after intervention (both P < 0.001). The proportion of sterile specimens increased from 30.43% before intervention to 34.84% after intervention, proportion of respiratory specimens decreased from 45.74% before intervention to 40.09% after intervention. The proportion of two or more sets of blood culture specimens increased from 18.63% before intervention to 21.95% after intervention (P < 0.001). Conclusion Application of comprehensive intervention measures can improve the submission rate and quality of clinical microbial specimens at the same time.