A novel heterogeneous catalyst system was obtained from the reaction of the molybdenum(VI) complex of 1,2-bis(2-formylphenoxymethyl)benzene with Fe3O4@SiO2–NH2 nanoparticles containing free amino groups on the surface groups. The complete characterization of catalysts was carried out by means of thermogravimetric analysis (TGA), scanning electron microscopy (SEM), transmission electron microscopy (TEM), vibrating sample magnetometry (VSM), X-ray photoelectron spectroscopy (XPS), elemental analysis, FT-IR and Raman microprobe techniques. The obtained nanoparticles were employed as catalysts for the selective oxidation of sulfides to corresponding sulfoxides using urea hydrogen peroxide as the oxidant. Furthermore, the obtained catalysts showed not only high catalytic activity in oxidation reactions but also high degree of chemical stability in various organic solvents. The immobilized molybdenum complex on silica coated magnetic nanoparticles can easily be recovered from the reaction system using an external magnet and reused several times with high yields. The thermogravimetric analysis (TGA) curve of the nanocatalyst shows the multistep mass loss of the organic materials between 50 and 600 C (Fig. 1). X-ray photoelectron spectroscopy (XPS) was applied to determine the oxidation state of the Mo content (Fig. 2).