This study developed a two-step method to prepare nitrogen-doped carbon microsphere-coated Fe3O4 by hydrothermal carbonization and potassium borohydride (KBH4) reduction methods deriving from xylose ferric chloride and urea. The obtained material (Fe3O4@C-BH) promoted the persulfate (PS) activation for degradation of organic contaminants. The nano-Fe3O4 particles were confirmed to be encapsulated in carbon spheres by systematic characterization. In virtue of the protective effect of carbon coating, the problems of being prone to agglomeration and oxidation of Fe3O4 were improved. Fe3O4@C-BH featured the effective catalytic performance to activate PS for RB5 degradation. The removal and mineralization rates of RB5 were 95.8% and 65%, respectively. The pH of the initial solution and the inorganic anions (Cl− and SO42−) had little effect on the degradation of reactive black 5 (RB5). Further, it performed high removal efficiency for Congo Red (CR), Rhodamine B (RhB) and tetracycline hydrochloride (TC). Notably, the increase of oxygen functional groups and Fe2+ content on the carbon surface by KHB4 modification was considered to be the main reason for improving catalytic activity. By analyzing electron paramagnetic resonance (EPR) and quenching experiments, SO4⋅−, ⋅OH and 1O2 were the primary active substances in oxidation process. A plausible mechanism was proposed in which the encapsulated Fe3O4 nano, oxygen functional groups and doped nitrogen synergistically drove PS activation to remove organic contaminants. It provides new insights into developing efficient core–shell carbon-based materials as PS activators for organic contaminants degradation in groundwater. [ABSTRACT FROM AUTHOR]