To guide the design of novel graphene-based catalysts in catalytic ozonation for micropollutant degradation, the mechanism of catalytic ozonation with heteroatom-doped graphene was clarified. Reduced graphene oxide doped with nitrogen, phosphorus, boron, and sulfur atoms (N-, P-, B-, and S-rGO) were synthesized, and their catalytic ozonation performances were evaluated in the degradation of refractory organics and bromate elimination simultaneously. Doping with heteroatoms, except sulfur, significantly improved the catalytic ozonation activity of graphene. Introducing sulfur atoms destroyed the stability of graphene during ozonation, with the observed partial performance improvement caused by surface adsorption. Degradation pathways for selected refractory organics were proposed based on the intermediates identified using high-resolution Orbitrap mass spectroscopy and gas chromatographic-mass spectroscopy. Three and six new unopened intermediates were identified in benzotriazole and p-chlorobenzoic acid degradation, respectively. Roles of chemical functional groups, doped atoms, free electron, and delocalized A. electron of heteroatom-doped graphene in catalytic ozonation were identified, and contributions of these active centers to the formation of reactive oxygen species (ROS), including hydroxyl radicals, superoxide radicals, singlet oxygen, and H2O2, were evaluated. A mechanism for catalytic ozonation by heteroatom-doped graphene was proposed for the first time.