The modulation of the shape and design of microstructures plays a crucial role in enhancing the efficient absorption of electromagnetic waves in absorbers. The electromagnetic parameters and scattering effects of these materials are directly influenced by their morphological characteristics. In this study, polystyrene microspheres were used as templates for a two-step in-situ growth process: Initially, Fe₃O₄ was coated onto the surfaces of these microspheres, followed by the in-situ growth of Fe-Co Prussian blue analogs. The rational design of electrical parameters during the conversion process was calculated and analyzed using Density Functional Theory. The precursor was calcined at various temperatures to generate a unique porous wrinkled surface hollow nanostructure. This nanostructure not only facilitates multiple reflections and scattering of incident electromagnetic waves but also promotes the occurrence of multiple interface polarizations. Doping with nitrogen and oxygen elements introduced abundant dipole polarization, thereby enhancing the electromagnetic wave attenuation capability of the composite material. The Fe3O4@PBA composite material synthesized at 600°C achieved a minimum reflection loss of −57.01 dB and a maximum effective absorption bandwidth of 4.58 GHz (7.52–12.1 GHz) at a thickness of 4 mm, covering nearly the entire X-band. This method provides a means to enhance magnetic loss by temperature adjustment to control the magnetic components in composite materials, providing a systematic approach to designing the microstructure of materials used for absorbing electromagnetic waves.