Objective To analyze the current status of underreporting of healthcare-associated infection (HAI) cases, identify high underreporting departments and infection types. Methods Based on multi-stage random sampling design, a retrospective survey was conducted on discharged patients from all clinical departments of the branch of a tertiary first-class general hospital in Jiangxi Province from February 1 to December 31, 2024. The occurrence and underreporting of HAI cases were judged by HAI management professionals, characteristics of HAI and underreported HAI cases were compared and analyzed. Results A total of 12 106 patients were surveyed, covering 33 clinical departments throughout the hospital. 157 cases of HAI were confirmed, the incidence was 1.30%; Among them, there were 77 underreported cases, with an underreporting rate of 49.04%. The incidence of HAI among different departments was statistically different (P<0.001), with intensive care unit (ICU) having the highest incidence (20.56%). The underreporting rate of HAI among different departments was statistically different (P<0.001), with the department of surgery having the highest underreporting rate (82.05%). Among the 157 HAI cases, the main infection sites were the lower respiratory tract (n=76, 48.41%), blood (n=24, 15.29%), and urinary tract (n=14, 8.92%), et al. There was no statistically significant difference in the underreporting rate of different infection sites (P=0.173). The underreporting rate of surgical site infection as well as skin and soft tissue infection were 83.33% and 66.67%, respectively. Conclusion The problem of underreporting of HAI is prominent, and it is urgent to strengthen doctors’ cognition on the definition, diagnosis, and reporting of HAI, optimize surveillance processes, coordinate performance management and reporting incentives for disease diagnosis-related group, and improve the authenticity of HAI surveillance data.