Refractory organic pollutant effluent has led to severe water pollution. In this study, magnetic Co–N-doped carbon hybrid catalysts (Co-NC-x) were fabricated using a facile cation exchange combined pyrolysis and self-reduction technique to activate peroxymonosulfate (PMS) for rehabilitation of the water environment. Factors affecting the catalytic activity of the Co-NC-850 were comprehensively examined. 100% of RhB degradation efficiency within 20 min was achieved in the Co-NC-850/PMS system at the optimum conditions (C0 = 80 mg L−1, catalyst loading 0.025 g L−1, PMS concentration 0.8 mM, native pH and 25 °C). The electron paramagnetic resonance measurements and competitive quenching tests demonstrated that a sulfate radical (SO4•-) and singlet oxygen (1O2) account for RhB degradation in the Co-NC-850/PMS system, and 1O2 contributed ~86.2% to RhB removal. The synergistic effect of Co0 nanoparticles (NPs) and NC on Co-NC-850 might induce a predominant non-radical route to trigger PMS activation for RhB degradation. Direct oxidation of O2•- by a hydroxyl radical (•OH) might be the crucial process for forming 1O2. Magnetic response and successive cycles verified that Co-NC-850 has superior separable performance and reusability. This innovative magnetic Co-NC-850 hybrid catalyst for PMS activation delivered vast potential for disintegration of refractory organic contaminants.