Constructing multifunctional aerogels that simultaneously integrate electromagnetic microwave (EMW) absorption, flame retardancy, acoustic damping, and thermal protection remains a formidable challenge due to inherent trade-offs in structural design and compositional synergy. Herein, we propose a hierarchical assembly and controlled carbonization strategy to fabricate MXene-reinforced MOF-on-MOF derived carbon aerogels (Z@F_xN_y-M/CA), wherein the Fe³⁺/Ni²⁺ molar ratio is precisely tuned to tailor the microstructure, defect chemistry, and interfacial characteristics. This design enables a unique synergistic interplay between a conductive MXene network, defect-rich carbon frameworks, and Fe/Co/Ni-derived magnetic components, collectively realizing efficient EMW attenuation via coupled conduction loss, polarization relaxation, and magnetic resonance. Remarkably, the optimized aerogel achieves an outstanding minimum reflection loss (RL_min) of -60.36 dB and a broad effective absorption bandwidth (EAB) of 5.06 GHz, outperforming most state-of-the-art absorbers. Beyond EMW absorption, the aerogel exhibits exceptional fire safety, with over 50% reduction in peak heat release rate (pHRR) and total heat release (THR), along with suppressed smoke emission and the formation of a dense graphitized char layer. Furthermore, it delivers superior acoustic damping with a noise reduction coefficient (NRC) of 0.66 and efficient thermal management capability. Such integrated multifunctionality is intrinsically linked to the finely engineered pore architecture, abundant heterogeneous interfaces, and compositionally modulated Fe/Co/Ni-derived phases. This work presents a paradigm-shifting MOF-on-MOF strategy for designing next-generation lightweight aerogels that harmoniously integrate EMW absorption, flame retardancy, thermal insulation, and acoustic protection, offering new insights into structure–property relationships in multimetal-derived multifunctional materials.