The deposition of gold nanoparticles on the magnetite (Fe3O4) surface is demonstrated through a molecular dynamics method. The simulated results show that an intermediate layer composed by such as a surfactant, polymer, or silica plays a key role in the formation of core/shell Fe3O4/Au nanostructures. The functional groups of the intermediate layer are crucial factors in depositing gold onto the Fe3O4 surface via nonbonding interactions, in which the van der Waals and Columbic forces will determine the strength of interaction toward the gold and iron oxide. Such interactions can affect the stability of the metal-coated nanocomposites and hence the functional properties. The nanocomposite is further investigated on the surface adsorption of amino acids (e.g., cysteine), which may be useful for functional exploration in biomedical applications.