With the increasing deterioration of the electromagnetic environment, it is important to develop new and efficient electromagnetic wave-absorbing materials. In this work, bilayer hollow HsGDY/NC nanotubes with controllable thickness are constructed by introducing high conductivity polydopamine (PDA) and hydrogen-substituted graphdiyne (HsGDY) followed by the etching and carbonization. Subsequently, the effects of the composition, coating order, and structural characteristics of nanotubes on the electromagnetic parameters are thoroughly investigated, thereby analyzing the microwave absorption mechanism. The impedance matching of HsGDY/NC is optimized by changing the thickness of NC layer, while utilizing unique multi-heterogeneous interfaces and hierarchical conductive structures that enhance the interface polarization and conductive loss. As a result, HsGDY@NC-3 displays the optimal absorbing performance with an effective absorption bandwidth (EAB) of 7.8 GHz (10.1–17.9 GHz) and a minimum reflection loss (RLmin) of −47.18 dB at the filler content of only 11 %. This work broadens the application scopes of HsGDY and provides a novel insight into the design of lightweight, high-efficiency, and wide-frequency microwave absorbers, which is expected to be a potentially effective microwave-absorbing material.