Single-atoms (SAs) strategies have been proved to be effective in modulating electromagnetic wave (EMW) absorption, however, the establishment of a definitive relationship between metal SAs electronic configurations and physical loss mechanisms has been still absent, especially on the atomic scale. Herein, stable Ni-SAsx/N-doped carbon (NC) absorbers are fabricated with the strategy of ligand polymerization. The morphology, composition, electrical conductivity, defects, and electronic interactions of the material can be well tailored by Ni species modulation engineering. Theoretical and experimental results show that the atomically dispersed individual Ni atoms contribute to enhanced EMW absorption performance through excess Ni 3d orbital unpaired electron induced polarization loss. Benefiting from it, Ni-SAs3/NC with the highest Ni SAy-Nx (y > 1, x > 1) polar/defect centers exhibit excellent EMW absorption with an effective absorption bandwidth of 7.08 GHz at a matched thickness of 2.50 mm. Radar cross-section simulations further demonstrate its potential for practical application as EMW absorber. This study reveals the continuous evolution of microscopic electromagnetic loss mechanism (i.e., conduction loss→ unique polarization loss→ conduction loss) for the first time, which provides insight into the deep design of absorbers from atom-scale view.