This study aimed to assess potential failure mode, implement countermeasures against risks and improve disinfection quality monitoring using healthcare failure mode and effect analysis (HFMEA).Between July 2017 and March 2018, a multidisciplinary team was formed to conduct HFMEA and implement improvement interventions. Fourteen monitoring departments and seven monitoring items were involved. The qualification rate of monitoring process was used to evaluate the influence of HFMEA on the standardization monitoring management of disinfection quality.After HFMEA, the qualification rate of overall monitoring process of disinfection quality improved from 16.5% to 78.7% (P < 0.001), and the qualification rates of each monitoring step were all significantly improved. The qualification rate implemented by the clinical laboratory improved from 20.1% to 100.0% (P < 0.001). The qualification rate implemented by thirteen monitoring departments improved from 20.1% to 78.7% (P < 0.001), where seven reached 100%. Out of seven monitored items, three had the qualification rate of 100.0%, while the remaining four items showed significant rising in qualification rates (P < 0.001).HFMEA were helpful in improving the qualification rate of disinfection effect monitoring process.