Objective To understand the management effectiveness of the intervention in multidrug-resistant organism (MDRO) infection through quality management tool plan-do-check-act (PDCA), and evaluate the impact in healthcare institutions under the diagnosis-related group/diagnosis-intervention packet (DRG/DIP) charging model. Methods The implementation of the prevention and control measures for MDRO infection in a tertiary first-class hospital from November 1 to December 31, 2021, and the infection-related indicators of the departments with high MDRO infection incidence were collected retrospectively. From March 1 to April 30, 2022, PDCA was adopted for intervention. The implementation rate of the prevention and control measures for MDRO infection, the incidence of healthcare-associated infection (HAI), the average length of hospital stay, and the average expense of hospitalization before and after the intervention were compared. Results The implementation rate of prevention and control measures for MDRO infection before and after PDCA intervention increased from 61.94% to 88.35%. After PDCA intervention, the incidence of MDRO HAI, the average length of hospital stay and the average hospitalization expenses of departments with high incidence of MDRO infection decreased compared with those before the intervention, with statistically significant differences (all P < 0.05). Conclusion The scientific use of PDCA can improve the implementation rate of the prevention and control measures for MDRO infection, and decrease the incidence of HAI and the average hospitalization expenses, as well as shorten the average length of hospital stay, thus avoid medical expense loss in medical institutions under the DRG/DIP charging mode.