Electromagnetic interference (EMI) shielding materials with low electromagnetic (EM) waves reflection characteristics are ideal materials for blocking EM radiation and pollution. Materials with low reflectivity must be constructed using materials with excellent EM waves absorption properties. However, materials simultaneously possessing both low reflectivity and excellent EMI shielding performance remain scarce, consequently, multilayer structures need to be developed. Poly(p-phenylene-2,6-benzobisoxazole) nanofibers (PNF) are prepared by deprotonation. PNF are combined with MXene and heterostructure MXene@Ni prepared by in-situ growth; MXene@Ni/PNF acts as an EM absorption layer while MXene/PNF acts as an EM reflective layer. Finally, (MXene@Ni/PNF)-(MXene/PNF) aerogels are prepared by layer-by-layer freeze-drying based on the layered modular design concept. Experimental characterizations revealed that (MXene@Ni/PNF)-(MXene/PNF) aerogels enable the efficient absorption-reflection-reabsorption of EM waves, effectively eliminating EMI. When the mass ratio of MXene to Ni in MXene@Ni is 1:6 and the mass fraction of MXene in the reflective layer is 80 wt.%, the (MXene@Ni/PNF)-(MXene/PNF) aerogels exhibit excellent EMI shielding performance (71 dB) and a very low reflection coefficient (R = 0.10). Finite element simulations verified that the developed asymmetric structural aerogels achieve high EMI shielding performance with low reflection characteristics. In addition, (MXene@Ni/PNF)-(MXene/PNF) aerogels display excellent infrared camouflage ability.