A novel magnetic nanocomposite of Au-Ag nanoparticles anchored on Fe3O4/graphene oxide spheres (Fe3O4/GO/Au-Ag) was successfully fabricated by the layer-by-layer assembly technique. The prepared Fe3O4/GO/Au-Ag was fully characterized by Fourier-transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD) analysis, thermogravimetric analysis (TGA), field-emission scanning electron microscopy (FE-SEM), energy-dispersive x-ray spectroscopy (EDS), transmission electron microscopy (TEM), and Raman spectroscopy. This nanocomposite showed unique catalytic performance for the synthesis of Spiro[indoline-3,5-pyrido[2,3-d:6,5-d’]dipyrimidine]-pentaone derivatives by the three-component condensation reaction of isatins, barbituric acids and 6-amino uracil at room temperature and in aqueous media. The significant advantages of this protocol include highly stable, easily separable and reusable catalyst, simple operation, environmental friendliness and excellent yields.