Despite the extensive research conducted on dielectric–magnetic coupling in metal-organic frameworks (MOF)-derived absorbers, the underlying mechanisms associated with defects, interfaces, and orbital hybridization remain inadequately investigated. To address this, we developed coral-like MOF-derived nickel–phosphorous@carbon (NP@C) nanocomposites by adjusting the pyrolysis temperature, revealing for the first time the link between structure and electromagnetic (EM) performance. The composite features nickel phosphide nanoparticles (Ni₁₂P₅ core/Ni₂P shell) embedded in an amorphous carbon matrix, where a unique crystal orientation and interfacial coupling enhance EM wave dissipation. The calculations show that charge transfer (0.66e) at the C–Ni₁₂P₅ interface increases conductance loss, whereas the C–Ni₂P–Ni₁₂P₅ heterostructure generates interfacial polarization and defect states via negative charge transfer (0.20e), synergistically enhancing dielectric and magnetic loss. Electronic structure analysis revealed that sharp Ni 3d orbital peaks near the Fermi level coexist with broad carbon matrix peaks, enabling both conductive and spin-related magnetic loss mechanisms. The NP@C nanocomposite achieves a reflection loss of −54.1 dB and an effective absorption band covering 4.1 GHz at a thin thickness of 1.37 mm. This study clarifies the atomic- and electronic-level EM response mechanisms of MOF-derived carbon materials, offering new insights for designing high-performance absorbers.