The XPS, XANES, and UV-Vis results revealed that oxygen vacancies were formed in the surface of MoO3/SiO2 by impregnation of the catalyst with citric acid followed by a temperature-programmed heating under N-2 atmosphere. The presence of the induction period during the oxidative desulfurization (ODS) of dibenzothiophene over these Mo-based catalysts using cumene hydroperoxide as the oxidant suggests that the reaction would follow a free radical mechanism. Both the higher ODS activity and the faster deactivation of the modified catalysts give evidences that the oxygen vacancies should possess a high ODS activity.