Ultrasound is a promising non-thermal inactivation technique. However, ultrasound treatment alone is not very effective. In this study, combined applications of ultrasound and non-thermal plasma (NTP) were assessed for their inactivation efficacy and the physiological change on Staphylococcus aureus cells. The lethal and sublethal injury induced by individual ultrasound, NTP, ultrasound-NTP (UP) and NTP-ultrasound treatments was determined by plate count method. Then, we applied fluorescent technology to demonstrate the physiological variations of S. aureus during various treatments. NTP exposure followed by ultrasound treatment exhibited the highest inactivation rate of S. aureus. Prior NTP helped to provide enough reactive oxygen species (ROS) dissolved in the medium, and the subsequent ultrasound assisted in the injection of ROS into S. aureus cells. This accelerated the reaction between ROS and intracellular biomolecules, which led to the rapid death of the microbes. On the contrary, S. aureus cells treated with ultrasound first were more likely to develop and enhance oxidative response, allowing S. aureus to resist toward the following NTP stressor. Therefore, the findings of this study may be used to the optimization of hurdle technologies of ultrasound and NTP in practice.