The flotation separation efficiency of pyrite and arsenopyrite can be enhanced by low-temperature oxygen plasma pretreatment. In this study, the plasma modification mechanism on arsenopyrite and pyrite and the effect on the flotation performance of pyrite and arsenopyrite were investigated. The results showed that plasma modification preferentially starts at the edges and rough areas of the arsenopyrite particles and results in substantial enrichment of O and depletions of Fe, As, and S on the mineral surface. After plasma modification, the concentration of sulfate species on the arsenopyrite surface increased significantly, which promoted the dissolution of the mineral surface and further reduced the number of collector adsorption sites (Fe). Flotation experiment results indicated that plasma modification has excellent selectivity, the arsenopyrite particles were completely hydrophilic and pyrite still exhibited excellent flotation performance.