MXene, as a rising star among two-dimensional (2D) electromagnetic wave materials, faces urgent challenges in addressing its self-stacking issue and regulating its conductivity. Herein, a micro-macro collaborative design strategy was proposed to regulate heterogeneous interface engineering in MXene-based absorbers. Biomass-based cotton was introduced as three-dimensional (3D) framework for constructing a porous structure, TiO₂ was in-situ generated and nitrogen atom was doped on Ti₃C₂T_x MXene to regulate its dielectric properties, a 3D N-doped carbon fiber/MXene/TiO₂ (CMT) nano-aerogel was successful constructed. The synergistic effects of diverse components and structural designs, porous frameworks and TiO₂ lattice contraction can significantly adjust the density of the conductive network and create abundant heterogeneous interfaces, as well as the lattice defects induced by nitrogen atom doping can enhance polarization loss, ultimately leading to the excellent microwave absorption performance of 3D N-CMT nano-aerogels. The optimized N-CMT 30% aerogel exhibited a minimum reflection loss (RL_min) of −72.56 dB and an effective absorption bandwidth (EAB) of 6.92 GHz at 2.23 mm. Notably, when the thickness was adjusted from 1 to 5 mm, the EAB of the N-CMT 30% aerogel reached 13.94 GHz, achieving coverage of 98% of the C-band and the entire X and Ku bands. Furthermore, the attenuation capabilities of the N-CMT aerogel were further confirmed through RCS simulations, whose RCS reduction value reaches up to 19.969 dB·m². These results demonstrate that 3D N-CMT nano-aerogel relying on interface engineering design exhibits significant potential in the field of electromagnetic protection, providing an important reference for future efficient absorbers.