Transition metal oxides can be used as efficient multiphase catalysts in the field of catalysis. In this study, a hydrophobic halloysite nanotube (HNT) catalyst was designed and prepared with a low loading. Tungsten oxide was immobilized on the inner surface of the HNT, through electrostatic adsorption and calcination. Furthermore, a dual-functional W/ HMT/M catalyst was prepared by hydrophobic modification of the outer surface of HNT through a harmless and nontoxic method. The catalyst was applied in the oxidative desulfurization (ODS) of dibenzothiophene (DBT), and characterized by inductively coupled plasma (ICP), contact angle tests, and other methods. Systematic characterization further confirmed that W/HNT/M has a low loading (0.48 wt %) and a relatively high contact angle of 92.6°. Oxidative desulfurization experiments demonstrated that the high contact angle corresponds to good hydrophobicity. The low loading and high activity of the catalyst enabled it to achieve a removal efficiency of 100% for DBT under conditions of 60 °C and an O/S = 4. The hydrophobic surface of HNT allowed better dispersion in the oil phase, while its hydrophilic inner cavity could adsorb H 2 O 2 and the converted dibenzothiophene sulfoxide, thereby reducing the subsequent extraction steps after oxidative desulfurization and enhancing the reaction environment for reactants and active oxygen. W/HNT/M maintained high activity for at least 5 cycles. Additionally, the potential mechanism of the catalyst in the aqueous ODS reaction was proposed. This study demonstrates that HNT-supported metal oxides have desulfurization potential and provides ideas for improving ODS catalytic activity of the ODS through low loading, high activity, and unique hydrophobicity design.