Objective To analyze the effect of healthcare failure mode and effect analysis (HFMEA) based control management for preventing multidrug-resistant organism (MDRO) healthcare-associated infection (HAI) outbreak. Methods A multi-disciplinary team (MDT) for management implementation was set up to retrospectively analyze patients admitted to the intensive care unit (ICU) of a hospital from June to December 2020. HFMEA model was used to assess the risk of MDRO HAI outbreak prevention and control, causes of high-risk failure mode was analyzed, targeted preventive measures were formulated and implemented from January 2021. Staff's hand hygiene, wearing and taking off isolation clothing, as well as MDRO HAI occurred in patients before and after implementation were compared. Results After the implementation of HFMEA, the risk coefficient of potential failure mode of MDRO HAI in ICU decreased significantly. Compared with before implementation, Staff's compliance rate of hand hygiene increased by 10.98%-14.12%; staff's compliance rate in wearing isolation clothing when contacting MDRO-infected patients and patients' bed units increased by 8.61%-15.21%; correct rate of wearing and taking off isolation clothing increased by 10.73%-18.43%; HAI rate in ICU, daily MDRO HAI rate, incidence of ventilator-associated pneumonia (VAP), incidence of central venous catheter-related bloodstream infections (CRBSI), and catheter-associated urinary tract infection (CAUTI) decreased. Conclusion Prospective assessment of HFMEA as well as intervention of MDRO HAI prevention and control measures can effectively reduce the incidence of MDRO HAI, thus preventing the outbreak of MDRO HAI.