Dual-metal modifications on SBA-16 silica were implemented to modulate the acidities and the distribution and dispersion of active phases for NiMo catalysts. The results showed that the acidity of S-H groups in S-edge sites can be promoted by B acid and further facilitate the DDS selectivity. The NiMo/AT-7.5 catalyst exhibits the highest HDS efficiency of 97.5% due to its appropriate acidity, highest proportion of MoS2 phase and concentration of S-edge sites. The kinetic and thermodynamic analyses were applied to investigate the intrinsic HDS reactivity for various catalysts. The results confirmed the existence of synergistic effect in the DBT HDS reaction. The B acid sites can further increase the desulfurization route (DS) of THDBT to CHB. A higher dispersion degree of MoS2 could improve DBT HDS efficiency. A high total concentration of S-edge and Mo-edge will indicate a high HDS efficiency. The S-edge/Mo-edge ratio and kDDS/kHYD could be correlated.