Objective To analyze the effect of risk assessment on healthcare-associated infection (HAI) management. Methods Risk assessment on 36 departments in a hospital in 2016 and 2019 was carried out respectively, results of two assessment was compared (including change in risk assessment factors, change in high-risk departments, change in the integrity of current management system and so on). In addition, influence of risk assessment on HAI management was evaluated, that is, the change in HAI-related indicators, such as incidence of HAI, incidence of multidrug-resistant organism (MDRO) HAI, hand hygiene compliance, hand hygiene accuracy rate, ventilator utilization rate, central line catheterization rate, urinary catheterization rate, incidence of ventilator-associated pneumonia (VAP), incidence of central line-associated bloodstream infection(CLABSI) and incidence of catheter-associated urinary tract infection (CAUTI). Results Risk assessment in 2019 showed that cardiac surgery intensive care unit (ICU), respiratory ICU, cardiology ICU, surgery ICU, department of nephrology, pediatric surgery, geriatric ICU, neonatal ICU and pediatric ICU were high-risk departments, among which pediatric ICU, neonatal ICU, pediatric surgery and nephrology were the newly increased risk departments in 2019. Risk levels in four high-risk departments (neurology, rheumatology and immunology, hematology, and urology) in 2016 decrased significantly. Compared with surveyed data of 2016, the integrity of current management system in 2019 was improved, incidence of HAI, incidence of MDRO HAI, incidence of CAUTI and urinary catheterization rate decreased significantly, hand hygiene compliance and accuracy rate improved significantly, difference were all statistically significant (all P<0.05). Conclusion Through the risk assessment, the key departments and risk factors that should be paid attention can be pointed out and intervention can be implemented, which can effectively promote the management of HAI and reduce the incidence of HAI.