Objective To explore the effect of risk assessment method on the incidence of healthcare-associated infection(HAI) in high-risk departments. Methods A hospital was selected as the research object, risk assessment of HAI management at the hospital and department level was carried out, high-risk departments and high-risk links were screened out, targeted intervention was performed. Patients hospitalized in April-June 2017 were as control group and those hospitalized in July-September 2017 were as intervention group, incidence of HAI between two groups was compared. Results Through risk assessment at the hospital level, department of critical care medicine was the department with the highest risk, risk assessment at the department level showed that without wearing isolation clothes when contacting isolated patients during diagnosis and treatment, without using sterile sheeting when catheterization, and low correct rate of hand hygiene were high-risk links in department of critical care medicine. Targeted intervention was performed, isolation clothing allocation rate for contacting isolated patients increased from 0 to 100%, compliance rate to wearing isolation clothing among medical staff increased from 0 to 97.62%, implementation rate of using sterile sheet for deep vein catheterization increased from 72.50% to 100%; hand hygiene correct rate increased from 85.00% to 96.59%. Incidence of HAI decreased from 5.90% to 2.64%, difference was statistically significant (P<0.05). Conclusion Implementing risk assessment management of HAI in medical institutions can effectively guide the prevention and control of HAI in high-risk departments, and improve the level of HAI management.