Disinfection of hazardous microorganisms that may challenge environmental safety is a crucial issue for economic and public health. Here, we explore the potential of a novel electrochemical disinfectant named plasma activated water (PAW), which was generated by nonthermal plasma, for inactivating Staphylococcus aureus (S. aureus). Meanwhile, the influence of bovine serum albumin (BSA) on the PAW disinfection efficacy was investigated. In the presence of BSA, PAW treatments achieved a reduction of S. aureus ranging from 2.1 to 5.5 Log, when without BSA it reached 7 Log. The sterilization efficacy depended on the PAW treatment time of S. aureus and plasma activation time for PAW generation. The results of electron spin resonance spectra showed the concentrations of hydroxyl radical (OH•) and nitric oxide radical (NO•) in water activated by plasma for 10 min (10-PAW) were higher than those in water activated by plasma for 5 min (5-PAW). Additionally, the physiological analysis of S. aureus demonstrated that the integrity of cell membrane, membrane potential, and intracellular pH homeostasis as well as DNA structure were damaged by PAW, and the molecule structure and chemical bonds of S. aureus were also altered due to PAW. Thus, PAW can be a promising chemical-free and environmentally friendly electrochemical disinfectant for application in the medical and food industries.