A novel strategy was reported for the fabrication of yolk-shell magnetic MFSVmS-Au nanocomposites (NCs) consisting of double-layered ellipsoidal mesoporous silica shells, numerous sub-4 nm Au nanoparticles (NPs), and magnetic Fe central cores. The hierarchical FSVmS NCs with ellipsoidal α-FeO@mSiO/mSiO as yolks/shells were first prepared through the facile sol-gel template-assisted method, and plenty of extremely stable ultrafine Au NPs were postencapsulated within interlayer cavities through the unique deposition-precipitation method mediated with Au(en)Cl compounds. Notably, ethylenediamine ligands were used to synthesize the stable cationic complexes, [Au(en)], that readily underwent the deprotonation reaction to chemically modify negatively charged mesoporous silica under alkaline conditions. The subsequent two-stage programmed hydrogen annealing initiated the in situ formation of Au NPs and the reduction of α-FeO to magnetic Fe, where the synthesized Au NPs were highly resistant to harsh thermal sintering even at 700 °C. Given its structural superiority and magnetic nature, the MFSVmS-Au was demonstrated to be a highly efficient and recoverable nanocatalyst with superior activity and reusability toward the reduction of 4-nitrophenol to 4-aminophenol, and the pristine morphology was retained after six recycling tests.