Deep eutectic solvents (DESs) are a new class of green solvents analogous to ionic liquids due to their biodegradable capacity and low cost. However, the direct extractive desulfurization of diesel oil by DESs cannot meet the government’s standard. In this work, amphiphilic polyoxometalates were synthesized and characterized by FT-IR and mass spectrometry. The oxidative desulfurization results showed that benzothiophene (BT) could be completely removed by employing a [(C₆H₁₃)₃P(C₁₄H₂₉)]₃PMo₁₂O₄₀, DES (ChCl/2Ac) and H₂O₂ system. It was also found that the organic cation of catalysts played a positive role in oxidative desulfurization. The reaction conditions, such as reaction temperature and time, the amount of catalyst and DES and H₂O₂/S (O/S) molar ratio, were optimized. Different sulfides were tested to determine the desulfurization selectivity of the optimal reaction system, and it was found that 97.2% of dibenzothiophene (DBT) could be removed followed by 80.7% of 4-MDBT and 76.0% of 4,6-DMDBT. After reaction, the IR spectra showed that the catalyst [(C₆H₁₃)₃P(C₁₄H₂₉)]₃PMo₁₂O₄₀ was stable during the reaction process and the oxidative product was dibenzothiophene sulfone (DBTO₂). Furthermore, the catalyst can be regenerated and recycled for four runs with little loss of activity.