A series of NiMo/FDU-12 catalysts with tunable pore diameters and mesostructures have been controllably synthesized by adjusting the synthetic hydrothermal temperature and applied for the hydrodesulfurization of dibenzothiophene and its derivative. The state-of-the-art electron tomography revealed that the pore sizes of FDU-12 supports were enlarged with the increase in the hydrothermal temperature and the mesostructures were transformed from ordered cage-type pores to locally disordered channels. Meanwhile, the MoS2 morphology altered from small straight bar to semibending arc to spherical shape and finally to larger straight bar with the change of support structures. Among them, FDU-12 hydrothermally treated at 150 °C possessed appropriate pore diameter and connected pore structure and was favorable for the formation of highly active MoS2 with curved morphology; thus, its corresponding catalyst exhibited the best HDS activity. Furthermore, it was indicated that the isomerization pathway could be significantly improved for HDS of 4,6-dimethyldibenzothiophene after the addition of aluminum, which was expected to be applied to the removal of the macromolecular sulfur compounds. Our study sheds lights on the relationship between support effect, active sites morphology and HDS performance, and also provides a guidance for the development of highly active HDS catalysts.