<p>Achieving optimal electromagnetic properties in composites requires fine-tuning of microstructure and composition, presenting both practical value and fundamental challenges. Through precisely controlled carbonization of polymer-coated Fe₃O₄@SiO₂ assembled units, this work elucidates the phase transition-mediated enhancement of electromagnetic wave absorption properties. Raspberry-like C/Fe₃O₄@SiO₂@DC magnetic microspheres are fabricated through a multi-step process involving bubble-assisted hydrothermal growth, silica coating, phosphonitrile polymerization, resin encapsulation, and controlled carbonization. The controlled carbonization temperature-mediated phase transformation from Fe₃O₄ to Fe₂SiO₄ within the microspheres serves to fine-tune both electromagnetic parameters and impedance matching behavior. The C/Fe₃O₄@Fe₂SiO₄@DC microspheres carbonized at 700°C exhibit exceptional electromagnetic wave absorption performance, attributed to: (i) the heterogeneous interfaces between dual-phase components, and (ii) the synergistic dielectric-magnetic loss mechanism. The optimized composite demonstrates exceptional microwave absorption performance, achieving a minimum reflection loss (<i>RL</i>_min) of −17.86 dB and an effective absorption bandwidth (EAB) of 6.03 GHz (11.5–17.5 GHz) at an optimal thickness of 2.2 mm. The synergistic combination of tailored composition, optimized interfaces, and controlled defects enables unprecedented EM wave attenuation, providing a blueprint for high-efficiency broadband electromagnetic wave absorbing materials.</p>