Pesticides are widely used in commercial goji Lycium barbarum cultivation to prevent damage of the delicate fruits by insects, potentially leading to insecticide and fungicide residues at levels dangerous to human health. In this study, removal of organophosphorus pesticide (OP) residues (i.e. omethoate and dichlorvos) from the surface of L. barbarum was conducted using a gas phase surface discharge (GPSD) plasma system. ICCD and GC-MS measurements showed that a homogeneous and uniform GPSD glow-like plasma could be achieved and the efficiency of OP residues degradation greatly depended on the applied voltage and plasma exposure time, with 99.55% and 96.83% efficiency recorded for omethoate and dichlorvos (DDVP), respectively after 30 min GPSD plasma exposure at the discharge voltage of 10 kV. FT-IR and chemical analysis of the intermediates produced during GPSD exposure revealed that the omethoate and DDVP molecules could be completely degraded into nontoxic species, at the appropriate dosage of GPSD plasma exposure, without compromising the quality of L. barbarum. Based on the experimental and simulation results, a mechanism of OP degradation attributed to energetic electrons and highly reactive species generated by GPSD plasma was proposed.