[Objective] To determine the effect of atmospheric pressure plasma jet on the inactivation of Pseudomonas aeruginosa, and to explore the sterilization mechanism of atmospheric pressure plasma jet. [Methods] The bactericidal effect of atmospheric pressure plasma jet was determined by plate counting method. Treated cells were examined by fluorescence microscope and transmission electron microscope. Soluble proteins were quantified and analyzed by SDS-PAGE electrophoresis. [Results] More than 99.9% P. aeruginosa cells were killed after the plasma treatment for 5 min. The cell wall and membrane systems of P. aeruginosa was broken as evidenced by leakage of cellular contents of proteins. Amounts of proteins was detected in supernatant after treatment for 2 min. [Conclusion] Atmospheric pressure plasma jet is able to destroy the cell integrity, which results in leakage of cellular contents and eventually kills P. aeruginosa effectively.