Various adsorption configurations of dibenzothiophene, a series of one and two methyl-substituted dibenzothiophenes and their hydrogenated derivatives on a MoS2 nanocluster, were studied using self-consistent density functional theory with generalized-gradient approximation. The objective was to explore the relationship between the structure and catalytic hydrodesulfurization reactivity of these sulfur molecules. The calculated adsorption energies indicated that flat adsorption was more energetically favorable over perpendicular adsorption, due to the interactions of the sulfur atom, the thiophene, and aromatic rings of the sulfur molecule with the molybdenum atoms on the catalyst surface. The adsorption energy in the flat adsorption mode decreased when the aromatic ring was saturated, while the adsorption energy in the perpendicular mode increased with progressive saturation of the dibenzothiophenes. In the flat adsorption mode, dibenzothiophene, 4-methyldibenzothiophene, 2,8-, 3,7-, and 4,6-dimethyldibenzothiophenes interacted similarly with the catalyst cluster, which indicated that methyl groups on the 4-and 6-positions did not hinder the sulfur molecules from binding flat onto to the catalyst surface. However, in the perpendicular adsorption mode, it can be clearly seen from total electron density distribution of the sulfur-molecule-MoS2 cluster complex, that methyl groups in the 4-and 6-positions prevented the bonding of the sulfur atom with the surface molybdenum atom. The plane of the aromatic ring system in these dibenzothiophenes was disturbed by hydrogenation of one or two aromatic rings. Ring puckering was more severe with methyl-substituted dibenzothiophenes, resulting in a reduction of steric hindrance and easier access of the sulfur atom to the catalyst surface through perpendicular binding. The atomic electron charge distribution by Mulliken population analysis, the bond lengths of the free sulfur molecule and adsorbed sulfur molecules, as well as the Mayer bond order of the S-Mo bond in perpendicular adsorption mode were also examined in this work in an attempt to understand the different hydrodesulfarization reactivities of these molecules.