Atomically dispersed metals on N-doped carbon supports (M–NxCs) have great potential applications in various fields. However, a precise understanding of the definitive relationship between the configuration of metal single atoms and the dielectric loss properties of M–NxCs at the atomic-level is still lacking. Herein, we report a general approach to synthesize a series of three-dimensional (3D) honeycomb-like M–NxC (M = Mn, Fe, Co, Cu, or Ni) containing metal single atoms. Experimental results indicate that 3D M–NxCs exhibit a greatly enhanced dielectric loss compared with that of the NC matrix. Theoretical calculations demonstrate that the density of states of the d orbitals near the Fermi level is significantly increased and additional electrical dipoles are induced due to the destruction of the symmetry of the local microstructure, which enhances conductive loss and dipolar polarization loss of 3D M–NxCs, respectively. Consequently, these 3D M–NxCs exhibit excellent electromagnetic wave absorption properties, outperforming the most commonly reported absorbers. This study systematically explains the mechanism of dielectric loss at the atomic level for the first time and is of significance to the rational design of high-efficiency electromagnetic wave absorbing materials containing metal single atoms.