Surface modification mechanism of pyrite via Fenton reagent and its response to Cu-S flotation separation was examined in a low-alkaline system using micro-flotation experiments, contact angle, UV–vis, SEM, DFT, XPS, and ToF-SIMS analysis. Flotation and contact angle results proved Fenton reagent could effectively separate chalcopyrite from pyrite at pH = 8. The adsorption rate of hydroxyl radical (•OH) on pyrite surface reached 83.28 %. The SEM results show that flocculent hydrophilic substances were produced on the surface of pyrite after oxidation. Further, DFT calculations results on the basis of interaction between •OH and the pyrite (100) surface showed that strong chemical bonds among the O atom of •OH and the Fe and S atoms on the pyrite surface formed. DMOL3 model and XPS analysis confirmed the oxidation products were primarily found in the form of Fe(OH)3, Fe2O3, Fe(OH)2, Fe2(SO4)3, FeOOH and SO42-, which considerably rejected the adsorption of dixanthogen. The peak intensities of FeOH+ and SO4- both increased to 2312 and 2506. The intensity of C2H5+ ion decreased from 4204 to 1009. Thus, the Fenton reagent triggered the formation of multitude hydrophilic species, and offered a simple access to the pyrite depression. This activity provided a viable option for the Cu-S flotation separation.