Recognizing the structural heterogeneity of Metal-N-C single atom catalysts (M-N-C SACs) and further revealing the impact of other metal phases that may be generated during the preparation process on the catalytic activity of SACs are essential for the rational design of M-N-C SACs. Through the post-Fe(III)-N coordination strategy, an extremely reactive heterogeneous Fe-N-C SACs including Fe-Nx coordinating sites and carbon-iron hybrids into the N-doped graphene-containing carbon nanoflakes (Fe3C/Fe-Nx@GCN) is designed at the atomic level. As a stabilized Fenton-like activator, the catalyst exhibits a high mass activity of 2.08 × 105 min−1 mol−1 for the catalytic oxidation of recalcitrant organic. The experiments and density functional theory (DFT) calculations reveal that specific type of N-coordinated Fe sites with a lower d-band center position is prone to Fe-oxo species production. However, the incorporation of carbon-iron hybrids induces charge redistribution in the active metal centers, further enhancing catalyst’s adsorption energy on peroxymonosulfate (PMS) and effectively modulating the reaction energy barriers. Additionally, the electron transfer pathway dominated by potential differences was confirmed by appropriate reactive substrate orbital energies. This study preferentially provides perspectives on the synergistic relationship between carbon-iron hybrids and Fe-Nx in PMS-AOPs and proposes the multiple-reaction pathways for eliminating pharmaceuticals from the source-separated urine.