Efficient and clean flotation separation of copper-sulfur has attracted soaring interest in the beneficiation of sulfide ore. The objective of this work was to examine the influence of calcium hypochlorite (Ca(ClO)2) oxidative modification on the flotation separation of chalcopyrite from pyrite in acid mine drainage (AMD) system. A maximum recovery difference of 69.70 % between both minerals was observed under the recommended conditions (initial pH = 8.5 ± 0.2, [Ca(ClO)2] = 100 mg/L, [EX] = 32 mg/L, and the volume ratio of AMD to pure water = 1:1). A high-grade concentrate with 77.35 % Cu recovery and 29.01 % Cu grade was obtained, demonstrated by mixed-mineral micro-flotation experiments. Analysis of Cu and Fe ions influence indicated that low concentrations of Fe3+ and Cu2+ favored the selective separation of pyrite and chalcopyrite. Moreover, analysis of the pulp ion concentrations showed that Ca(ClO)2 promoted the dissolution of iron ions on the pyrite surface compared to chalcopyrite, thereby enhancing pyrite oxidation. The Ca(ClO)2 interacted more intensively with the pyrite surface, forming a passivated layer that impeded the adsorption of collector, as demonstrated by Zeta potential and contact angle results. The generation of hydrophilic products caused by oxidation on the pyrite surface, such as CaSO4, CaOH+, Fe(Ⅲ)–OOH, and/or Fe2(SO4)3 was confirmed by XPS analysis, further reducing the floatability of pyrite. Furthermore, local electrochemical impedance spectroscopy and scanning electron microscopy analyses further afforded favorable evidence for selective inhibition of pyrite by Ca(ClO)2 in the AMD system. This study provides a new approach to achieve cleaner separation of pyrite and chalcopyrite and offers new perspectives for AMD treatment solutions.