Series ZSM-5/SBA-16 (ZS) composites were prepared using various inorganic cations as additives, and the associated catalysts were tested for dibenzothiophene and 4,6-dimethyldibenzothiophene hydrodesulfurization (HDS). The structure function relationship was investigated through various characterization methods. The NiMo/ZS-Mg catalyst using MgCl2 as an additive displayed higher HDS reaction rate constant and turnover frequency values, which could be attributed to its major acidity, higher metal support interaction (MSI), higher sulfidation degree, higher dispersion degree, moderate stacking number, and shorter stacking length of sulfide Mo species, of which the higher acidity and higher MSI contributed more to the improvement of its HDS performance. Besides, the possible HDS pathways on the NiMo/ZS-Mg catalyst were provided.