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.