The CoMo type and NiMo type catalysts with high amounts of Bronsted (B) acid sites, referred to as FHUDS-5 and FHUDS-6 respectively, were investigated for their hydrogenation performances including alkylation, hydrodesulfurization (HDS), and hydrodenitrogenation (HDN). The results demonstrated that, as hydroprocessing different diesel feedstocks, appropriate types of catalyst or their stacking system should be considered to achieve optimal HDS performance. As processing the feedstock with high sulfur content but low contents of nitrogen and aromatics, the CoMo type FHUDS-5 exhibited the highest HDS efficiency. On the other hand, the NiMo type catalyst FHUDS-6 presented the highest HDS and HDN efficiency as processing the feedstock with high amounts of nitrogen and aromatics. As processing the feedstock with medium contents of nitrogen and aromatics, the catalysts stacking system of FHUDS-6/FHUDS-5 presented the highest HDS efficiency due to their synergistic effects. The commercial applications for these hydroprocessing catalysts for the ultra-deep HDS on diesel at different refinery plants were also reported.