With the increasingly strict limitations on emission standards of vehicles, deep desulfurization in fuel is indispensable for social development worldwide. In this study, a series of hybrid materials based on SiO2-supported polyoxometalate ionic liquid were successfully prepared via a facile ball milling method and employed as catalysts in the aerobic oxidative desulfurization process. The composition and structure of prepared samples were studied by various techniques, including FT-IR, UV-vis DRS, wide-angle XRD, BET, XPS, and SEM images. The experimental results indicated that the synthesized polyoxometalate ionic liquids were successfully loaded on SiO2 with a highly uniform dispersion. The prepared catalyst (C16PMoV/10SiO2) exhibited good desulfurization activity on different sulfur compounds. Moreover, the oxidation product and active species in the ODS process were respectively investigated via GC-MS and ESR analysis, indicating that the catalyst can activate oxygen to superoxide radicals during the reaction to convert DBT to its corresponding sulfone in the fuel.