Oxidative desulfurization(ODS) is an effective method for obtaining fuels that contain ultra-low sulfur. The purpose of this paper is to prepare a novel and effective bifunctional heterogeneous catalytic system for the desulfurization process by using nanorods cryptomelane octahedral manganese oxide molecular sieve(nanorod-OMS-2) and molybdenum oxide as active components. The MoOX/nanorod-OMS-2 catalysts were synthesized with different molybdenum loadings. The catalytic activities were evaluated for oxidative desulfurization of dibenzothiophene (DBT) in the presence of H2O2 and acetonitrile. Results of characterization analyzes showed that the synthesized catalysts contain the conventional surface area, pore-volume, mixed micro-mesoporous structures, and the molybdenum oxides species highly dispersed on the nanorod-OMS-2 surface. A synergistic effect was observed between Mn and Mo species which created strong acidic sites. In addition, the activity of catalysts is dependent on the composition of meso-microporous structures and the presence of strong acidic sites due to the interactions between the Manganese-molybdenum oxide species. In optimum condition over the Mo(7.5 wt%)/nanorod-OMS-2 catalyst, the percentage of sulfur removal was achieved to 99%. The kinetic of ODS reaction was studied, and the pseudo-first-order rate law was obtained with respect to DBT. The reusability of Mo(7.5wt%)/nanorod-OMS-2 was studied and the efficiency of catalyst has decreased from 99% to 98% during three cycles. The effects of oxidant/sulfur molar ratio, reaction time, reaction temperature were studied, and the optimum values were 8:1, 2h and 65 °C, respectively.