Objective To explore clinical effect of failure mode and effect analysis in improving the submission rate of pathogen examination in counterpart supported high-altitude county hospitals, and formulate practical measures and methods suitable for high-altitude county hospitals to improve the submission rate of pathogen examination. Methods Patients admitted to the People’s Hospital of Ganzi County between January and December 2024 were selected. The data of hospitalized patients between January and June 2024 were as the control group, and the data of hospitalized patients between July and December 2024 were as the intervention group. The study analyzed and compared the submission rate of pathogen testing and the pass rate of microbiological test specimens before antimicrobial treatment between the two groups. Results A total of 3 984 patients were included. Among them, there were 1 748 cases in the control group and 2 236 cases in the intervention group. A total of 10 risk factors and 2 high-risk points were identified. There were statistically significant differences in the submission rate of pathogen specimens before antibiotic treatment [36.21% (633/1 748) vs. 49.33% (1 103/2 236); χ2=68.646, P<0.001] and the qualified rate of microbiological test specimens [26.75% (122/456) vs. 36.45% (261/716); χ2=11.910, P=0.001] between the control group and the intervention group. Conclusions Failure mode and effect analysis can effectively find out the weak points in low pathogen examination submission rate in high-altitude county hospitals. According to the high-risk points to guide the formulation of relevant measures, the pathogen submission rate in the region can be effectively improved.