A universal gas diffusion strategy was developed to derive highly efficient PMS-activation catalysts comprising isolated Fe atoms coordinated with N species embedded in carbon polyhedrons (Fe-NC). Their electronic and geometric structures were modulated by altering the precursor ratio and calcination temperature. Benefiting from the maximized atomic utilization, the obtained catalysts exhibited superior catalytic performances, outperforming almost all previously reported metal materials. The enhanced activity is likely due to an optimal particle size and Fe content, favorable Fe-Nx active sites, and conductive carbon materials. Scavenging and probing experiments indicated that surface Fe-NC and the defective edges with oxygen functional groups were the active sites for PMS activation to produce surface-bonding active complexes (Fe-NC-PMS) and high-valent iron oxo species (FeV = O) for organic degradation, unlike the reported radicals and singlet oxygen mediated degradation. Overall, this work provides a universal gas diffusion strategy to design dimension-controlled Fe-NC catalysts for the elimination of organic pollutants.