Objective To evaluate the effectiveness of pharyngeal swabs combined with anal swabs as multidrug-resistant organism (MDRO) admission screening for patients in intensive care unit (ICU), and provide reference for healthcare-associated infection (HAI) prevention and control strategies. Methods Patients who underwent MDRO admission screening by pharyngeal swabs combined with anal swabs within 24 hours of admission to an ICU of a hospital in Shanghai from August 1 to December 31, 2022 were included as the experimental group, and those who underwent MDRO admission screening only by pharyngeal swabs from August 1 to December 31, 2021 were as the control group. Positive rate of screening, occurrence and pathogen of HAI between the two groups, as well as the sensitivity and specificity of combined admission screening for MDRO in the experimental group were compared. Results A total of 917 patients were included in the study, with 442 cases in the experimental group and 475 cases in the control group. The positive rates of admission screening for MDRO in the experimental and control groups were 7.40% and 3.37%, respectively. The incidences of HAI with MDRO in the experimental and control groups were 2.71% and 5.68%, respectively. Incidences of digestive system HAI with MDRO in the experimental and control groups were 0.68% and 2.32%, respectively. Differences were all statistically significant (all P < 0.05). The area under the ROC curve of admission screening by pharyngeal swabs combined with anal swabs for predicting HAI with MDRO in patients were 0.897 (P < 0.01, 95%CI: 0.802-0.993). The sensitivity and specificity of admi-ssion screening for MDRO by pharyngeal swabs combined with anal swabs in the experimental group were 72.73% and 97.65%, respectively. Conclusion The combination of pharyngeal swabs and anal swabs can be used as an ICU admission screening method for MDRO, and has an important clinical application value.