In refractory apical periodontitis, Enterococcus faecalis (E. faecalis) is most frequently detected, its biofilm is closely related to disease progression. Therefore, controlling E. faecalis infection in root canals is crucial for treatment success. The commonly used irrigation and disinfection methods for root canal include agent disinfection such as sodium hypochlorite and calcium hydroxide, as well as ultrasonic irrigation disinfection. At present, technologies such as development of new agents and photodynamic therapy are gradually applied in clinical practice and show promising prospects. This paper reviews the recent irrigation and disinfection methods for controlling E. faecalis root canals infection of refractory apical periodontitis both domestically and internationally, including traditional methods, new technologies, and their combined applications, aiming to provide reference for clinical infection control.