The effects of combined microwave and hydrogen peroxide (H₂O₂) oxidation on the flotation separation of molybdenite and chalcopyrite, as well as the underlying mechanism were investigated via microflotation, zeta potential, contact angle, X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and atomic force microscopy (AFM) analyses. The microflotation experiments showed that the effective inhibition of chalcopyrite can be obtained through combined oxidation pretreatments with low microwave power and H₂O₂ consumption. The zeta potential, contact angle and XPS analyses indicated that the surface hydrophobicity of molybdenite changed minimally after different treatments, whereas significant amounts of hydrophilic oxidation species were formed on the surface of chalcopyrite, thus decreasing its surface hydrophobicity and floatability. Moreover, the SEM and AFM analyses indicated that more uniform oxidative products were formed on the chalcopyrite surface, further significantly increasing the surface roughness.