Various Keggin-type heteropolyoxometalate catalysts with structural defects and surface acidity were synthesized by immobilizing 12-phosphotungstic acid (HPW) on mesoporous SBA−15, to produce near-zero-sulfur diesel fuel. As the calcination temperature increased, the W=O and the corner-shared W–O–W bonds in the Keggin unit partially broke, creating oxygen defects, as evidenced by the Rietveld refinement and in situ FTIR characterization. All the catalysts contained Lewis (L) and Brønsted (B) acid sites, with L acidity predominant. The relative intensity of the IR band (I980) of W=O bond inversely correlated with the number of L acid sites as the calcination temperature varied, suggesting that oxygen defects contributed to the Lewis acid sites formation. In the oxidation of dibenzothiophene (DBT) in a model diesel within a biphasic system, DBT conversion exceeded 99% under the optimal reaction conditions (reaction temperature 70 °C, reaction time 60 min, H2O2/sulfur molar ratio 8, H2O2/formic acid molar ratio 1.5, catalyst concentration 2 mg/mL). The influence of fuel composition and addition of indole and 4,6-DMDBT on DBT oxidation were also evaluated. Indole and cyclohexene negatively impacted the DBT oxidative removal. Oxygen defects served as active centers for competitive adsorption of sulfur compound and oxidant. Both L and B acid sites were involved in transferring O atom from peroxophosphotungstate complex to sulfur in DBT, resulting in DBTO2 sulfone, which was immediately extracted by polar acetonitrile. This study confirms that structural defects and surface acidity are crucial in the deep oxidative desulfurization (ODS) reaction, and in enabling the simultaneous oxidation and separation of refractory organosulfur compounds in a highly efficient model diesel.