We have presented a two-layer ONIOM study on the unimolecular and bimolecular hydrodesulfurization (HDS) mechanisms of thiophene catalyzed by H-Beta, H-MCM-22, H-ZSM-5, and H-FAU zeolites. The rate-determining step for HDS is the hydrogenation step. The bimolecular desulfurization mechanism is more favorable to occur due to the lower free energy barriers, which is in good accord with experimental observations. Hammond's postulate was validated by analyzing the thermodynamics and geometrical structures of transition states (TSs). The difference charge density (DCD), reduced density gradient (RDG), localized orbital locator (LOL), and Fukui functions were used to understand the nature of the TSs. For the dimerization step of two thiophene molecules, the DCD analysis indicates a dramatic electron transfer from the thiophene fragment to the hydrothiophene fragment in the TS. High LOL values between two α-C atoms of two thiophene rings indicate a strong interaction and a high degree of covalence between these two C atoms. For the step of H 2 S formation, a DCD analysis suggests a clear electron transfer from the H 2 S fragment to the organic carbon chain in the TS; the plots of RDG and LOL indicate a weak interaction between the C atom of the organic chain and the H 2 S fragment. The confined nanospace in zeolite has important stabilization effects on TSs and intermediates. The calculated results suggest that almost all the reaction steps in the unimolecular and bimolecular mechanisms on four zeolites are entropy-decreased processes. The stabilization effect of the ZSM-5 framework mainly originates from the VDW attractive interactions. The classic electrostatic interactions favor the formation of all the TSs on MCM-22. In the bimolecular mechanism, the behaviors of TSs in Beta are contrary to those in ZSM-5; the electrostatic interactions favor the formation of TSs over FAU, but no clear variation trend of VDW interactions is found.