An array cold atmospheric pressure plasma jet (ACAPPJ) apparatus with 4 × 4 channels and coverage area over than 6 cm2 was developed to decontaminate toxic chemicals on material surfaces using Helium (He) gas as discharge gas. Experimental results indicated that 20.4 mg aniline on 6.25 cm2 stainless steel plate could be totally decontaminated within 3 min when the ACAPPJ was conducted under 20 kV, 15 kHz, 10 L/min gas flow and 1.5 cm distance. The decontamination efficiency of malathion was not as good as aniline, but addition of H2O and O2 could apparently improve the decontamination performances. The decontamination rate of malathion could be improved from 45% to 95% when 1% H2O and 1% O2 were simultaneously introduced with He into the ACAPPJ system. ACAPPJ could even decontaminate the malathion penetrated into wood or rubber materials. The decontamination of aniline and malathion were the first order kinetic reactions, in which the·OH and O3 formed in the ACAPPJ played major roles. The decontamination of aniline was mainly electrophilic and ring opening reactions, while the malathion was mainly decontaminated due to the breaking of PS and S-C bonds. The intermediate products of aniline and malathion could be mineralized into CO2 and H2O when they were decontaminated by ACAPPJ for enough time. According to the nude mouse skin experiments, the ACAPPJ could be directly applied on animal skins without any electrical and chemical harms.