Biomass-derived carbon aerogels have emerged as promising electromagnetic protection materials due to their ultralight, porous, and eco-friendly properties, yet achieving high performance with environmental durability remains challenging. Employing an electromagnetic synergistic strategy, this work successfully fabricated a lotus seedpod-inspired carbon-based aerogel composite (SPCA@Co) using shaddock peel biomass, where magnetic Co components were introduced via zeolitic imidazolate framework (ZIF)-67. The material’s natural hierarchical porous structure and Co nanoparticle-anchored heterogeneous interfaces optimize impedance matching by regulating conductivity, polarization, and magnetic loss, yielding exceptional electromagnetic protection performance: −52.5 dB minimum reflection loss (RL_min) of 4.52 GHz effective absorption bandwidth (EAB) at 1.4 mm thickness, and 76 dB shielding efficiency. Simultaneously, SPCA@Co exhibits multifunctionality in complex environments, integrating thermal insulation, hydrophobicity, mechanical robustness, and stability under acid rain/weathering, with adaptability validated by radar cross-section simulations. This work provides a sustainable strategy for designing high-performance, multifunctional electromagnetic protections using biomass resources.