A detailed theoretical study of desulfurization mechanisms of thiophene and benzo thiophene was performed under inert and oxidative atmospheres. Density functional theory (DFT) was used to investigate the 13 reaction pathways of their desulfurization mechanisms under these two atmospheres. The feasibility of each reaction was analyzed thermodynamically and kinetically. The calculated results show that it is thermodynamically and kinetically unfavorable for thiophenes to desulfurize under inert atmosphere, if a H2 directly attacks their S atoms and C-S bonds. This is resulted by their extremely high energy barriers and high reaction energies. However, the desulfurization mechanisms of thiophenes may be thermodynamically dominated by Diels-Alder reaction under inert atmosphere. Compared with inert atmosphere, it is much easier for thiophenes to desulfurize under oxidative atmosphere. The reason is that C-S bond strength of thiophenes-OH and sulfones is much lower than that of thiophenes based on Mayer bond order (MBO) analysis. It is found that thiophenes oxidation desulfurization is very possibly initiated by oxidative agent OH rather than thiophenes C-S bond directly attacked by O2. In addition, Diels-Alder reaction between thiophene sulfones can also possess very low barrier reaction pathways.