Structural design and composition adjustment are promising approaches for the preparation of lightweight absorbers with high absorption performance and low matching thickness. In this work, a carbon nanotube-modified CoNi@MoO2/C composite was synthesized by ion-exchange, in-situ growth, and pyrolysis methods. For the synthesized CoNi@CNTs@ MoO2/C composite, the minimum reflection loss value (RLmin) was −63.2 dB at a thickness of 2.3 mm, and the effective absorption bandwidth reached 8.8 GHz (9.2–18 GHz) at a thickness of 2.5 mm. The potential microwave absorption mechanism is attributed to the synergistic effects of polarization relaxation, electron transmission, ferromagnetic resonance, as well as multiple reflections and scattering in the hierarchical nanocomposite. In addition, the radar cross-section (RCS) attenuation was calculated via HFSS to analyze the EMW absorption capacity in the actual far field. The RCS reduction was 36 dB m2 for a scattering angle of 0°. Overall, this work provides theoretical support for the controlled growth of metal-catalyzed CNTs and presents an effective guide for optimizing the electromagnetic and absorption performances of MA materials.