An atmospheric helium dielectric barrier discharge is used to treat Staphylococcus aureus (S. aureus) to study plasma bacteria inactivation in the gas-liquid phase. Optical emission spectroscopy, mass spectrometry, and spectrophotometry are used to analyze the products induced by the plasma in the liquid as well as interactions between the liquid products and bacteria. The bactericidal mechanisms associated with the liquid products and different treatment protocols are investigated. The short-lived reactive species produce efficient inactivation effects in the direct plasma treatment and long-lived reactive species show continuous residual bactericidal effects. Additionally, even the minor initial damage caused by direct plasma exposure promotes the residual inactivation effect. After the discharge treatment for 1, 3, 5, and 8 min, the initial damage causes residual bacterial inactivation of 9.3, 37.2, 81.8, and 86.7%, respectively. Meanwhile, the discharge time and storage time in the different treatment processes can be optimized to achieve better bactericidal efficiency and energy efficiency. The results provide insights into the future development of plasma medicine and water purification.