In view of the potential health risks caused by COVID-19 to rural small-scale sewage treatment facilities, the sterilization effect and effluent characteristics of commonly used treatment processes in rural areas, including constructed rapid infiltration (CRI), Anoxic/oxic (A/O) activated sludge and biofilm method, anaerobic biological treatment combined with constructed wetland and membrane bio-reactor (MBR) method were analyzed and compared. Based on the current disinfection techniques of sodium hypochlorite, chlorine dioxide and ultraviolet light, the corresponding disinfection processes, parameter selection and related risk prevention and control measures were put forward. This study can provide a reference for the safe operation of rural small-scale sewage facilities during the pandemic prevention and control period.