The effect of pulsed electric fields (PEF) on the reduction of the population and on the occurrence of sublethal injury of Staphylococcus aureus was investigated. Flow cytometry (FCM) in combination with PI and cF fluorescent was used for quantitative and real time detection of PEF induced damage on S. aureus cells and sublethally injured microbial cells. This work investigated that the occurrence of sublethal injured cells might depend on the electric field intensity. The occurrence of sublethally injured microbial cells in PEF treatment could seriously affect the food safety shelf life of PEF-treated foods. It is effective to synergistically combine PEF with other device to reduce the occurrence of sublethally injured microbial cells and extend the microbiological shelf life of PEF-treated foods.