A series of mesoporous materials of SBA-16 were in situ incorporated into ZSM-5 crystallites via a two-step self-assemble method, and hydrodesulfurization (HDS) catalysts were prepared on the corresponding ZSM-5/SBA-16 (ZS) composites. The characterization results indicated that ZSM-5 nanoseeds were fabricated into the silica framework of the ZS composites, and the three-dimensional Im3m cubic structure of SBA-16 was retained simultaneously. In addition, the ZS series materials possessed open pores and large surfaces, which would facilitate the diffusion of reactants in the mesoporous channels. Moreover, the introduction of ZSM-5 seeds into composites could enhance the acidities of supports. As a result, the NiMo/ZS series catalysts exhibited high activities for DBT HDS processes. The NiMo/ZS-160 catalyst exhibited the highest catalytic efficiency (96.5%), which was apparently attributed to the synergistic contributions of the physicochemical properties of ZS supports and the dispersion states of active metals. Correspondingly, DBT HDS reactions over the NiMo/ZS series catalysts mainly proceeded via a hydrogenation desulfurization route that benefitted from the enhanced acidities especially the total Brønsted acid.