For boosting the intrinsic peroxymonosulfate (PMS) catalytic activity of single atom catalysts (SACs), we fabricate zeolitic imidazolate framework (ZIF)-derived Fe SAC with different nitrogen coordination numbers (denoted as Fe-Nx/C) to boost organic pollutant oxidation. X-ray absorption fine structure (XAFS) spectroscopy was undertaken to determine the coordination configuration of Fe–N path. As expected, the resultant Fe-N3/C exhibited more excellent PMS catalysis activity with a p-nitrophenol (4-NP) degradation kinetic rate constant (kobs) of 0.061 min−1 that is 2.4-fold enhancement relative to the Fe-N4/C. Electron paramagnetic resonance (EPR) measurements and quenching tests confirmed the 1O play the main role associated with high-valent Fe–oxo and a small amount of OH and SO4− species. Density functional calculations revealed that low coordinated Fe–N3 sites prefer to form a bridge coordination bond structure of O-Fe-O with the adsorption sites of O2 and O1 in PMS molecule, exhibiting stronger interaction with the oxidant and better electron donating capability to enhance PMS activation comparing to common Fe-N4 structure based on charge deformation density, electron localization function (ELF) and projected density of state (PDOS) analysis. These findings indicate that microstructure modulation is a useful avenue to prepare a high-performance Fenton-like SACs.