Manipulating the electronic structure and geometric coordination environment of single metal atoms has been considered as promising approach for enhancing dipole polarization and enriching electromagnetic attenuation mechanisms. However, achieving precise control of the dielectric polarization response at atomic scale remains a huge challenge. Herein, a metal‐acetate coordination complexes‐assisted strategy is proposed to prepare spatially isolated cobalt (Co) atoms embedded in accordion‐like nitrogen‐doped carbon (NC) matrix. The interactions between metal atoms and NC matrix are carefully tailored through the successive evolution of dispersion states of Co species, ranging from individual atoms to atomic clusters to nanoparticles. Density functional theory reveals that the orbital hybridization between the d electrons of embedded Co atoms and p electrons of coordinated N atoms induces the electron redistribution at N sites, enabling enhanced electric dipole polarization and robust room temperature magnetism (a saturation magnetization of 0.108 emu g−1 at 300 K). Consequently, Co‐SAs@NC exhibits optimal electromagnetic wave absorption properties with a minimum reflection loss of ‐54.4 dB and an effective absorption bandwidth of 8.4 GHz. This work demonstrates an efficient strategy for modulating electromagnetic response at atomic level and provides a novel insight into the d/p electrons orbital hybridization between single metal atoms and NC species.