Atomically dispersed transition metal-nitrogen-carbon (M-N-C) is regarded as one of the prospective materials to eliminate organic pollutants in water. However, manipulating the coordination sphere of the center metal to achieve the highest catalytic performance remains a challenge. Herein, a Fe-BNC catalyst with Fe atom decorated B,N-codoped hierarchical porous carbon was synthesized for peroxydisulfate (PDS) activation, which exhibits superb and highly selective degradation of model aqueous pollutants within a wide pH scope (2.63–10.36). The experiments and theoretical simulation indicate that the high activity of Fe-BNC origins from novel dual-pathway activation, involving PDS oxidation at the electron-poor B atoms for the formation of singlet oxygen (1O2) and PDS reduction over electron-rich Fe atoms for the generation of hydroxyl and sulfate radicals, where 1O2 was the primary active species. Moreover, the B atoms introduces point defects and optimizes the distribution of Fe 3d orbitals, which simultaneously facilitates PDS chemical adsorption and activation. We further loaded Fe-BNC on the widely used polyvinylidene fluoride (PVDF) microfiltration membrane and proved the stable performance for removing model pollutants when they pass through the filter, advancing the applications of M-N-C materials in actual practice.