Honeycomb structural composites were fabricated by impregnating aramid paper frame with modified whisker carbon nanotubes (CNTs) and polyurethane resin (PU). CNTs were oxidized by using mixed acid and strong oxidant. Vector network analysis was used to measure the reflection loss (RL) of the honeycomb composites and the compressive test of honeycomb composites was carried out with a universal testing machine. For the double-layers honeycomb composites, the method of concentration gradient design can bring double absorption peak resonance benefit, which expand the microwave absorption bandwidth. Therefore, RL achieves the absorption bandwidth (< -10 dB) of 14 GHz covering 4–18 GHz for double-layer honeycomb composites. In addition, an effective model is proposed through the logarithmic law and equivalent circuit theory. The absorption property of the composites is attributed to the quarter-wavelength cancellation interference and multiple scattering, harmonic peaks move to a low-frequency stage with the increase of the CNTs average content. Compared to pristine double-layers honeycomb core, the compression strength and the elastic modulus are enhanced by 64% and 123%, respectively. The composites benefiting from the excellent mechanical and absorption performance have significant potential in stealth technology fields.