Series Al-SBA-16 supports with different crystal sizes were fabricated by adding different inorganic salts to the synthesis system and used as the catalyst support for dibenzothiophene (DBT) and 4,6-dimethyldibenzo-thiophene (4,6-DMDBT) hydrodesulfurization (HDS). The supports and the corresponding catalysts were well analyzed in depth to investigate their structure property relationship. NiMo/AS-Mn catalyst with the smallest crystal sizes, the largest BET surface areas, and the highest total acid and Bronsted acid content displayed the highest k(HDS) of 4,6-DMDBT and DBT. HYD was the preferential route for the DBT HDS over NiMo/AS-Mn, while ISO was the preferential pathway for 4,6-DMDBT HDS. Moreover, the DBT and 4,6-DMDBT HDS reaction networks over NiMo/AS-Mn were proposed.