Objective To observe the effectiveness of department of healthcare-associated infection(HAI) management actively participating in the management of clinical application of antimicrobial agents. Methods Changes in evaluation index of clinical application management of antimicrobial agents before(2012-2014) and after (2015-2017) department of HAI management actively participated in management was compared. Results After department of HAI management actively participated in management of clinical application of antimicrobial agents, the utilization rate of antimicrobial agents in hospitalized patients decreased from 17.18% before active management to 15.24%, the utilization rate of special used antimicrobial agents decreased from 1.45% to 1.02%, microbial detection rate before antimicrobial use in patients receiving special grade antimicrobial agents increased from 87.12% to 91.15%. After active management, antimicrobial prophylaxis rate in patients undergoing class Ⅰ incision operation was 10.86%, administration rate 0.5-1 hour before operation was 89.32%, 86.77% of patients received<24 hour course of antimicrobial prophylaxis, all were higher than 8.74%, 75.87%, and 57.81% respectively before active participation, differences were all statistically significant (all P<0.001). Before active management, surgical site infection(SSI) rates of class I, II, and III incision were 0.27%, 0.92%, and 1.29% respectively, after active management, SSI rates were 0.20%,0.67%,and 4.42% respectively. There was significant difference in SSI rate of class II incision before and after active management (P=0.011). Conclusion Active participation of the department of HAI management in antimicrobial management can obviously improve the evaluation index of clinical application of antimicrobial agents, and promote the rational use of antimicrobial agents.