The purpose of this study is to explore the impact of multi-departmental linkage and rational drug use supervision on the drug resistance of pathogenic bacteria in primary hospitals. Use the method of pharmacies and infection control departments to jointly develop hospital antimicrobial usage guidelines and reward and punishment systems to promote the rational use of antimicrobial drugs. In addition, clinicians and clinical pharmacists of the pharmacy department participated in the formulation of anti-infection programs, infection control departments and pharmacy supervision, and compared the rational use of antibacterial drugs, the time of antibacterial drug use, and the detection of drug-resistant bacteria between the two groups before and after the implementation of the mechanism. Our results showed that the rational use rates of medication indications, drug selection, drug dosage, and medication course in the observation group were 97.74%, 96.99%, 98.50%, and 96.24%, respectively, which were higher than 79.71% in the control group, 76.81%, 72.46% and 75.36%, the difference was statistically significant (P < .05); there was no statistically significant difference in the rational utilization rate of drug administration routes between the two groups (P > .05). The antibacterial drug use time of the observation group was (7.39±1.84) d shorter than that of the control group (13.53±2.61) d, and the difference was statistically significant (P < .05). The detection rate of drug-resistant bacteria in the observation group was 24.44%, which was lower than 42.86% in the control group, and the difference was statistically significant (P < .05). This shows that the grassroots multi-department linkage supervision mechanism is in line with the management model of standardizing the rational use of antimicrobial drugs at the grassroots level, and the intervention in the application of antibacterial drugs is conducive to improving the knowledge reserve of drug use among the grassroots people. The economic cost of reducing drug-resistant bacteria is huge. In addition to death and disability, long-term illness can result in longer hospital stays, the need for more expensive medications, and a significant financial burden on those affected. Therefore, improving the rationality of clinicians' medication use will help shorten treatment time and reduce drug-resistant bacteria. It is worthy of clinical promotion and application.