Silicon carbide/carbon (SiC/C) composites have shown great promise as high-temperature electromagnetic wave absorbers, yet their practical application remains limited due to inherent impedance mismatch. In this study, a polymer-derived strategy for synthesizing three-dimensional porous Co-doped SiC/C aerogels using silicon-arylacetylene resin (PSA) as the precursor was reported. The precursor solution was prepared via a thiol-yne click reaction combined with coordination between Co ions and alkyne groups, which was subsequently processed through ambient-pressure gelation, freeze-drying, and pyrolysis to obtain the final aerogel. Co enhances electrical conductivity and optimizes dielectric loss through lattice doping into intrinsic silicon vacancies (V_Si), while simultaneously introducing additional magnetic loss via metallic Co nanoparticles generated by carbothermal reduction. Furthermore, Co catalyzes the in-situ growth of worm-like SiC nanowires, constructing multiple heterogeneous interfaces. This integrated modulation strategy effectively improved impedance matching and established a synergistic dielectric-magnetic loss mechanism. The optimized aerogel exhibited outstanding microwave absorption performance, achieving a minimum reflection loss (RL_min) of −61.51 dB at 13.10 GHz and an effective absorption bandwidth (EAB) of 4.70 GHz at an ultrathin thickness of 1.3 mm. This work provides an innovative route for developing transition-metal-doped porous materials and offers an effective strategy for designing high-performance electromagnetic wave absorbers with tailored properties.