MY-x series zeolites with different mesopore diameters were successfully synthesized via a hydrothermal synthesis procedure and the corresponding NiMo/HMY-x series hydrodesulfurization(HDS) catalysts were prepared via incipient co-impregnation method. The synthesized samples were characterized by both wide and small angle XRD, N-2 adsorption-desorption isotherms, pyridine adsorbed FTIR (Py-FTIR), Al-27 MAS NMR, H-2-TPR, HRTEM and XPS. The results show that the synthesized samples exhibit wide opened mesopores of varying sizes with well crystallized pore walls. The introduction of mesopores caused a slight decline in the interaction between active metals and support (MSI) in the corresponding catalysts, generating higher stacking numbers and a shorter slab lengths among MoS2 crystals on the corresponding catalyst and favoring both the dispersion and sulfidation of Mo species, particularly favoring the formation of both active edge sites and highly active corner active sites. The reaction network for 4,6-DMDBT HDS over NiMo/HMY-x series catalysts is proposed, and HDS selectivity is found to be related to mesopore size. More specifically, HYD activity is linearly correlated to the number of Mo atoms located along the edge sites of MoS2 crystals, and DDS activity is linearly correlated with the number of Mo atoms located at the corner sites of MoS2 crystals. Finally, the active corner sites are approximately 10 times more active than active edge sites.