Abstract: The development of graphene-based microwave absorbing materials featuring low filler loading, thin thickness, wide bandwidth, and strong absorption is currently a prominent research focus. However, achieving an effective synergy between impedance matching and attenuation capability at low filler loadings remains a formidable challenge. To address this issue, a strategy for the synergistic regulation of graphene-based multi-loss systems at the atomic scale is innovatively proposed. By employing a simultaneous introduction strategy of urea and Fe³⁺/Ni²⁺ salts, nitrogen-doped reduced graphene oxide composites co-modified with FeNi₃ nanoparticles and Ni-N_x coordination sites (FeNi₃/Ni-N-RGO) are successfully synthesized through freeze-drying-assisted precursor construction followed by high-temperature carbonization. This rational design enables the synergistic coupling of magnetic components and dielectric regulation centers, where FeNi₃ nanoparticles provide magnetic loss while highly dispersed Ni-N_x sites serve as polarization centers to effectively induce enhanced dipolar and interfacial polarizations. Results demonstrate that at a remarkably low filler loading of only 2.3wt.%, a minimum reflection loss of −54.93 dB is achieved at a matching thickness of 2.6 mm within the 2-18 GHz range, accompanied by an effective absorption bandwidth of 4.6 GHz at a thickness of 1.7 mm. Structural characterization and electromagnetic parameter analysis confirm that the multi-scale magnetic-dielectric synergy between FeNi₃ and Ni-N_x enhances both interfacial polarization and conduction loss. This study provides a new approach for the development of lightweight and high-efficiency microwave absorbing materials.