Aerobic oxidative desulfurization of a model diesel fuel over MOx/CNTs catalysts (M = Ce, Cu, Mo) was studied to develop innovative technology for cleaning motor fuels to EURO-5 standard. It was shown that the thermal stability of catalysts improves in the following order of metal Сu < Сe < Мо. The disordering of the carbon matrix of support increases in the next row of M: Mo < Ce < Cu, which is accompanied by an increase in the specific surface area of the samples (40 → 105 m2/g). The forms of stabilization of the active component (CeO2, CuO/Cu2O/ Cu, or MoO3/MoO2) were revealed, indicating a partial reduction of the metal cations during the thermal decomposition of copper and molybdenum precursor compounds deposited on CNTs. In oxidative desulfurization of a model diesel fuel over MOx/CNTs catalysts at 150 °C the total conversion of dibenzothiophene increased in the next row of M: Се < Сu < Мо. It was found that at 150 °C over the optimum MoOx/CNTs catalyst the highest dibenzothiophene conversion 95–99% is observed. It was assumed that the high activity of MoOx/CNTs is associated with both the oxidizing ability and the tendency of MoOx to chemosorption of sulfur compounds.