The synergistic effect of magnetic loss and dielectric loss, as well as the reasonable construction of microstructure, have a significant effect on improving the absorption performance of electromagnetic wave absorbers. In this paper, N-doping Co@ carbon nanotubes (NCC) composites are successfully grown in situ on cobalt particles using a cobalt source as a catalyst. The metal particle Co is encapsulated within the carbon nanotubes and N is doped in the carbon lattice. This special structure introduces a large number of heterogeneous interfaces and defects, leading to optimized impedance matching and strong electromagnetic attenuation. The results showed that the minimum reflection loss is −69.33 dB for NCC800-1 with a thickness of 1.6 mm, and NCC900-4 possesses the widest effective absorption bandwidth of 7.70 GHz at a thickness of 2.1 mm with other NCC composites. Furthermore, the radar scattering cross section simulation results confirm that the prepared absorbing coatings can well suppress radar waves in different directions. The outstanding absorption performance is attributed to the defects and heterogeneous interfaces in the cobalt-catalyzed carbon nanofibers, the conductive network formed by carbon fibers, and the synergistic effects of magnetic and dielectric losses. This work presents a novel engineering approach for synthesizing absorbers with multiple loss mechanisms and heterogeneous structures, offering a promising pathway for the development of high-performance electromagnetic wave absorbing materials.