The synthesis of highly efficient and stable catalysts for oxidative desulfurization is still a challenging task. Herein, a composite material ([email protected]) of phosphomolybdic acid (HPMo) encapsulated in the metal-organic framework UiO-66 with missing-linker defects was prepared via a one-pot hydrothermal method. A series of as-synthesized catalysts were systematically characterized by XRD, FT-IR, SEM, BET, TGA, XPS, UV–vis and PL. Through oxidative desulfurization experimental evaluations, the catalyst [email protected] with defects shows the superior catalytic oxidative desulfurization performance and high reusability. [email protected] is able to completely remove DBT in the model fuel in 60 min, and the reaction system can be recycled 10 times with a high activity. In addition, the kinetics and the activation energy of the oxidative desulfurization were studied.