Nontoxic nanoparticle contrast agents with multiple imaging functions are required for medical diagnostic imaging, and coating the nanoparticle contrast agents with less toxic materials meets this requirement. This work proposes a method for fabricating magnetite, gold (Au), and silica nanoparticles toward diagnostic imaging. The proposed method involved four steps: the synthesis of magnetite (Fe3O4) nanoparticles, synthesis of Au nanoparticles, formation of a composite of Fe3O4 and Au (Fe3O4/Au), and silica coating of Fe3O4/Au nanoparticles. The synthesis of 6.3 ± 1.2 nm-sized Fe3O4 nanoparticles was performed via a salt-based reaction in an aqueous solution containing FeCl3, FeCl2, citric acid, HCl, and NaOH. The synthesis of 2.2 ± 0.4 nm-sized Au nanoparticles was performed with a reduction of HAuCl4 in an aqueous solution containing tetrakis (hydroxymethyl) phosphonium chloride, and NaOH. The silica coating of Fe3O4/Au nanoparticles was performed with a sol–gel reaction in ethanol containing Fe3O4 nanoparticles, Au nanoparticles, poly-diallyldimetheylammonium chloride, tetraethylorthosilicate, NaOH, and water under sonication. The Fe3O4/Au/SiO2 nanoparticles were degraded in a fetal bovine serum/phosphate-buffered saline solution, PEGylated Fe3O4/Au/SiO2 (Fe3O4/Au/SiO2–PEG) nanoparticles adsorbed protein after PEGylation, and Fe3O4/Au/SiO2–PEG nanoparticles had a magnetic property and an X-ray imaging ability, revealing that the composite nanoparticles were expected to function as a safe and excretable contrast agent of MRI and X-ray.