Bimetallic Mo-M (M = Ni, Co, and Zn)/RHY supported catalysts were synthesized for oxidative desulfurization (ODS) of dibenzithiophene (DBT). Recrystallized HY zeolite (RHY) included a superior meso-porous structure (RHY) which is attractive for bulky dibenzothiophene (DBT) elimination. The facilities of M promoters on the Mo/RHY features and activity were investigated. Despite similar ionic radius, different electronegativity of Ni, Co, and Zn transition metals caused to different interaction with Mo and RHY zeolite. The results demonstrated that Ni influenced negatively on dispersion of Mo species over the support, while Co and Zn improved the dispersion. Ni interacted readily with framework Al, leading to extraction of Al, collapse of the zeolite structure, and more octahedral and crystalline Mo species. The formation of MoO3 crystals was inhibited by Zn and Co addition leading to improvement of Mo dispersion. Moreover, Zn- and Co-doped Mo/RHY exhibited higher Lewis acidic sites. The ODS activity decreased in the order of MoZn > MoCo > Mo > MoNi. UV–vis results approved that the most of Mo in the Zn doped sample was non-framework type which can well disperse over the external surface. Meanwhile, Co addition enhanced the tetrahedral Mo species incorporated into the zeolite framework. Allowing more exposed high active Mo species for ODS reaction by Zn promoter, the catalytic performance was boosted. The best catalyst, MoZn/RHY, exhibited 100% DBT removal (t = 30 min, T = 40 ◦C, catalyst/fuel = 10 g/L, O/S = 10, VSolvent/VOil = 1/2, DBT = 1000 ppm) and a high reusability in 4 consecutive recycles. The highest removal of indole as a nitrogen compound was also achieved by the introduced MoZn/RHY catalyst.