Surface modulation strategies have spurred great interest with regard to regulating the morphology, dispersion and flexible processability of materials. Unsurprisingly, customized modulation of surfaces is primed to offer a route to control their electronic functions. To regulate electromagnetic wave (EMW) absorption applications by surface engineering is an unmet challenge. Thanks to pyrolyzing surface-anchored metal-porphyrin, here we report on the surface modulation of four-nitrogen atoms-confined single metal site on a nitrogen-doped carbon layer (sM(N4)@NC, M = Ni, Co, Cu, Ni/Cu) (sM=single metal; NC= nitrogen-doped carbon layer) that registers electromagnetic wave absorption. Surface-anchored metal-porphyrins are afforded by attaching them onto the polypyrrole surface via a prototypical click reaction. Further, sM(N4)@NC is experimentally found to elicit an identical dipole polarization loss mechanism, overcoming the handicaps of conductivity loss, defects, and interfacial polarization loss among the current EMW absorber models. Importantly, sM(N4)@NC is found toexhibit an effective absorption bandwidth of 6.44 and reflection loss of -51.7 dB, preceding state-of-the-art carbon-based EMW absorbers. This study introduces a surface modulation strategy to design EMW absorbers based on single metal sites that enable fine-tunable and controlled absorption mechanism with atomistic precision.