The highly active and durable design of heterogeneous catalysts holds vital importance in the popularization of Fenton-like process for wastewater remediation. In this study, we successfully fabricated magnetic N-doped graphitic carbon (NC) encapsulated Fe3C/Fe nanoparticles, designated as Fe3C/Fe@NC-2.8, with a two-step pyrolysis method. We employed chitosan as a green precursor of NC, which is used as a heterogeneous Fenton-like catalyst to degrade refractory organic pollutants. Density functional theory (DFT) calculations revealed that the built-in electric field from the shell to core promoted electron transfer from NC to Fe3C/Fe, and thereby improved regeneration of Fe(II) and H2O2 activation. Because of the strong synergistic effects of the dual-reaction regions of Fe and Fe3C, as well as the core-shell structure advantages, the optimized Fe3C/Fe@NC rapidly degraded the typical refractory organic pollutants, and showed a much higher activity than the reference Fe2O3 and Fe3O4 samples. The total organic carbon removal efficiency of bisphenol A reached 70 % after reaction for 60 min. In addition, Fe3C/Fe@NC-2.8 possessed trace Fe leaching and satisfactory magnetically separable ability. This work provides mechanistic and practical perspectives for the development of advanced catalysts for recalcitrant pollutant treatment.