By using density functional theory (DFT) calculation and dispersion corrections of DFT-D method, the stacking effect of unsupported multilayer NiMoS nanocluster on hydrodesulfurization (HDS) of 4,6-dimethyldibenzothiophene (4,6-DMDBT) via direct desulfurization (DDS) route is investigated. We establish multilayer NiMoS nanocluster by stacking the monolayer active phase according to former characterization. The results show that the activation energy of C-S bond cleavage on dilayer is about 60 kJ∙mol−1 than that of monolayer in case I and near 160 kJ∙mol−1 higher in case II, moreover, it is about 300 kJ∙mol−1 higher on trilayer model. It seems DDS of 4,6-DMDBT could only occur at the corner sites of the top or bottom layer of regular multilayer NiMoS. Besides, the hydrogen transfer from the adjacent layer is also investigated in case IV and V of dilayer and trilayer, respectively. However, the activation energies of case IV and V are both over 400 kJ∙mol−1, which makes the reactions unlikely to happen. Overall, the stacking effects of unsupported multilayer NiMoS cause severe steric hindrance in the process of C-S bond cleavage, hydrogen transfer and CH bond formation. Therefore, only the monolayer model is the most efficient surface in catalyzing DDS of 4,6-DMDBT and usage of active metals, the dilayer model is barely acceptable and the multilayer model (layer ≥ 3) is unnecessary.