With the aim of deep desulfurization, silica-supported polyoxometalate-based ionic liquids were successfully prepared by a one-pot hydrothermal process and employed in heterogeneous oxidative desulfurization of various sulfur compounds. The compositions and structures of the hybrid samples were characterized by various methods such as FT-IR, XPS, Raman, UV–Vis, wide-angle XRD and N₂ adsorption–desorption. The experimental results indicated that the hybrid materials presented a high dispersion of tungsten species and excellent catalytic activity for the removal of 4,6-dimethyldibenzothiophene without any organic solvent as extractant, and the sulfur removal could reach 100.0% under mild conditions. The catalytic performance on various substrates was also investigated in detail. After cycling seven cycles, the sulfur removal of the heterogeneous system still reached 93.0%. The GC-MS analysis results demonstrated that the sulfur compound was first adsorbed by the catalyst and subsequently oxidized to its corresponding sulfone.