The future implementation of ultralow sulfur fuel regulations requires researchers to have an excellent understanding of the mechanism of the synergistic effect between the Co(Ni) and (Mo)W sulfides in supported Co(Ni)Mo(W)S hydrodesulfurization (HDS) catalysts. This synergistic effect occurs when the distance between two metals is on the mm or nm scale. To investigate the promotion of HDS on the µm scale, a series of Co and Mo multilayer flake catalysts with a thickness of 1 mm were prepared by laminate molding. The distance between CoSx and MoS2 in these specially structured catalysts was adjustable on the µm scale by controlling the order and quality of the catalyst powder. The results for the HDS of dibenzothiophene (DBT) demonstrate that there is an obvious synergistic effect between CoSx and MoS2 on the µm scale. The results of pyridine IR spectroscopy indicate that this synergy is due to CoSx and MoS2 synergistically generating more coordinatively unsaturated sites (CUSs) and -SH active sites at the μm scale, thus increasing the HDS activity. Moreover, the catalyst activity increases as the distance between CoSx and MoS2 decreases, and the fact that the feed comes into contact with CoSx first greatly improves the activity.