In this study, the sterilizing effect of atmospheric pressure nonequilibrium plasmas (APNPs) on Neisseria gonorrhoeae (N. gonorrhoeae) was preliminarily examined and the possible mechanisms were explored. N. gonorrhoeae FA1090, FA19 and MSll were treated by APNPs and their survival rate was analyzed by using CFUs counting and structurally studied by laser scanning confocal microscopy. The morphological changes of bacterial cell membrane and wall were studied under TEM. Our results showed that APNPs had strong sterilizing effect on N. gonorrhoeae. The survival rate of MS11 in N. gonorrhoeae liquid medium was 60.65% after disinfection with the APNPs for 5 rain, whereas, the survival rate of FA19 was 92.60% and the rate of FA1090 was 96.40%. The survival rate of MS 11 was 21.13% after exposure to APNPs for 6 rain, whereas the survival rate of FA19 was 31.60% and the rate of FA1090 was 91.00%. N. gonorrhoeae was structurally damaged after treatment with APNPs. It is concluded that APNPs is able to effectively and quickly kill the N. gonorrhoeae, and the killing effect is related to the architectural damage of cell membrane.