Effect of pore structure on the activity and stability of sulfide phase in hydrodesulfurization (HDS) of diesel were systematically investigated. A series of alumina with different pore structure were prepared by calcining pseudo boehmite at different temperatures. Various characterizations suggested that the surface concentration of OH groups and Lewis acid sites generally decreased with calcination temperature. The properties of sulfide phase in fresh and spent catalysts were analysis by X-ray photoelectron spectroscopy (XPS) and high resolution transmission electron microscopy (HRTEM). The results showed that the concentration of CoMoS species was greatly decreased after the reaction while the average length of MoS2 slabs was substantially increased. The concentration of preserved CoMoS species was proportional to the average pore size of support indicating that the stripoff of Co from CoMoS phase can be reduced when the average pore size is larger. Furthermore, the activity evaluation showed that larger pore structure of support is beneficial for the intrinsic activity and stability of CoMoS phase in the HDS of diesel. The reason was partially attributed to that the pore with larger diameter can reduce the coke deposition on the catalyst so that increase the intrinsic activity and stability of CoMoS sites.