Objective To understand the current situation of healthcare-associated infection(HAI) in Inner Mongolia, and provide basis for formulating management measures for HAI. Methods According to the requirement of national HAI surveillance network in 2018, all tertiary and secondary general hospitals and specialty hospitals in Inner Mongolia voluntarily participated in cross-sectional survey on prevalence rate of HAI, independently selected survey date and filled in unified questionnaire. Results In 2018, a total of 169 hospitals in Inner Mongolia participated in prevalence rate survey, 61 469 patients were investigated. 1 016 patients had 1 100 cases of HAI, prevalence rate and case prevalence rate of HAI were 1.65% and 1.79% respectively. Prevalence rates of HAI in hospitals ≥ 900 beds was 2.60%. The top three departments with higher prevalent rates of HAI were general intensive care unit (ICU) (12.70%), department of hematology (6.55%), and neonatal group of department of pediatrics (5.98%). The main HAI sites were lower respiratory tract (44.82%), urinary tract (16.82%), and upper respiratory tract (10.82%). Antimicrobial usage rate was 28.04%, there was a significant difference in antimicrobial usage rate among hospitals of different sizes (χ²=650.353,P<0.001). Pathogenic detection rate of patients with therapeutic antimicrobial use was 36.08%. The larger scale of hospitals, the higher rate of pathogenic detection in patients with therapeutic antimicrobial use, difference was statistically significant(χ²=449.309,P<0.001). The top three departments with higher therapeutic antimicrobial use were non-neonatal group of department of pediatrics (n=1 821, 98.11%), department of respiratory medicine (n=2 463, 97.62%) and department of nephrology (n=334, 96.53%); department with more antimicrobial use were departments of obstetrics (n=484, 82.59%), departments of gynecology (n=395, 66.72%) and departments of orthopaedics (n=1 106, 64.68%). A total of 457 pathogens causing HAI were detected, including 325 strains (71.12%) of gram-negative bacteria, 82 (17.94%) gram-positive bacteria and 30 (6.57%) fungi. The main pathogens causing HAI were Klebsiella pneumoniae (n=82), Escherichia coli (n=81), and Pseudomonas aeruginosa (n=76). Conclusion The prevalence rate of this survey is lower than the whole country and other regions. HAI management departments can take effective measures to prevent and control infection in key departments and main infection sites, and improve pathogenic detection rate of therapeutic antimicrobial use in small hospitals.