Controlling phase composition and interfacial structures in electromagnetic waves (EMWs) absorbing composites is a promising approach to enhance the absorption efficiency and integrate multifunctional properties. Here, we report the fabrication of iron-based nanostructured heterojunctions on reduced graphene oxide (rGO) via freeze-drying and controlled thermal treatment, enabling precise modulation of iron oxide phases. Among the obtained composites, the Fe₃O₄/Fe@rGO hybrid exhibited the strongest EMWs absorption. This enhancement originates from multiple loss mechanisms at the Fe₃O₄/Fe heterointerfaces, yielding a minimum reflection loss of −66.4 dB at 2.7 mm and an effective absorption bandwidth (EAB) of 7.16 GHz. Furthermore, a metal surface designed via full-wave simulations broadens the EAB to 15.3 GHz through optimized impedance and multi-resonance. The flexible Fe₃O₄/Fe@rGO film demonstrated high-performance infrared stealth, hydrophobicity, and efficient electromagnetic interference shielding. Density functional theory calculations revealed pronounced charge transfer at Fe₃O₄/Fe interfaces. Radar cross-section simulations further confirmed the material’s potential to substantially reduce detectability. This work presents a robust design strategy for next-generation electromagnetic protection materials with tunable composition, strong EMWs absorption, and integrated multifunctionality.