Amphiphilic hybrid catalysts were prepared by modifying [SMoO] with tetrabutylammonium bromide (TBAB), 1-butyl-3-methylimidazole bromide (BMIMBr) and octadecyl trimethyl ammonium bromide (ODAB), respectively. The prepared catalysts were characterized by IR, XRD, SEM, TG and XPS. The desulfurization performance of the catalysts was investigated in model oil and actual diesel using hydrogen peroxide (HO) as an oxidant and acetonitrile as an extractant. All catalysts exhibited favorable activity for removing sulfur compounds at room temperature. Dibenzothiophene (DBT) can be nearly completely removed using SMoO-organic catalysts within a short reaction time. For different sulfur compounds, the [TBA]SMoO catalyst showed a better removal effect than the [BMIM]SMoO and [ODA]SMoO catalyst. The [TBA]SMoO dissolved in extraction solvent could be reused up to five times in an oxidative desulfurization (ODS) cycle with no significant loss of activity. The [BMIM]SMoO performed as a heterogeneous catalyst able to be recycled from the ODS system and maintained excellent catalytic activity. The catalysts showed a positive desulfurization effect in real diesel treatment. Finally, we described the ODS desulfurization mechanism of DBT using SMoO-organic hybrid catalysts. The amphiphilic hybrid catalyst cation captures DBT, while SMoO reacts with the oxidant HO to produce peroxy-active species. DBT can be oxidized to its sulfone by the action of peroxy-active species to achieve ODS desulfurization.