Antibiotic resistant bacteria (ARB) and resistance genes (ARGs) are emerging environmental pollutants with strong pathogenicity. In this study, surface plasma was developed to inactivate the donor ARB with Escherichia coli (AR E. coli) as a model, eliminate ARGs, and inhibit conjugative transfer of ARGs in water, highlighting the influences of concomitant inorganic ions. Surface plasma oxidation significantly inactivated AR E. coli, eliminated ARGs, and inhibited conjugative transfer of ARGs, and the presence of NO3−, Cu2+, and Fe2+ all promoted these processes, and SO42− did not have distinct effect. Approximately 4.5log AR E. coli was inactivated within 10 min treatment, and it increased to 7.4log AR E. coli after adding Fe2+. Integrons intI1 decreased by 3.10log (without Fe2+) and 4.43log (adding Fe2+); the addition of Fe2+ in the surface plasma induced 99.8% decline in the conjugative transfer frequency. The inhibition effects on the conjugative transfer of ARGs were mainly attributed to the reduced reactive oxygen species levels, decreased DNA damage-induced response, decreased intercellular contact, and down-regulated expression of plasmid transfer genes. This study disclosed underlying mechanisms for inhibiting ARGs transfer, and supplied a prospective technique for ARGs control.