Due to the increasingly serious environmental problems caused by the combustion of sulfides in fuel, deep desulfurization of fuel became particularly urgent. Herein, the catalyst (PMA@MOF-808) of the Zr-based metal-organic framework (MOF-808) encapsulating phosphomolybdic acid (PMA) was prepared via a one-pot hydrothermal method. Besides, the formate ions of PMA@MOF-808 were removed by posttreatment with methanol, resulting in formate-free PMA@MOF-808-H catalysts with unsaturated open metal sites. The as-synthesized catalysts were systematically characterized by XRD, FT-IR, SEM, BET, TGA, H NMR and XPS. The catalysts were also applied in catalytic oxidation desulfurization of fuel. The results indicated that the introduction of PMA and the removal of formate ions can improve the desulfurization performance of catalysts. Formate-free 0.2-PMA@MOF-808-H catalyst can reach 100% desulfurization rate for DBT. Besides, the kinetic properties were studied, and the apparent activation energy was 29.34 kJ/mol.