The desulfurization offluid catalytic cracking (FCC) gasoline by alkylation over solid acid catalysts is considered to be a viable and less costly path to meet environmental regulations of sulfur emissions. However, side reactions in the process lead to significant levels of coke, which will greatly reduce the lifetime of the catalyst. In this paper, the catalytic mechanism of MCM-41 supported phosphoric acid catalyst for gasoline desulfurization by alkylation has been investigated by using experimental methods and quantum chemical calculations to study the catalytic behavior for the adsorption and reaction of different reactants, which can help optimize the reaction conditions and preparation methods of the catalyst for a more efficient alkylation process. The results showed that both the typical main and side reactions in the alkylation process started from a stable alkoxide intermediate that was formed by protonation of olefin adsorbed on the catalyst. Thiophenic compounds were more inclined to be adsorbed on the alkoxide intermediate than olefins for further reaction, and the activation energy for the alkylation of thiophenic sulfurs with alkenes was obviously lower than that for alkene oligomerization. Moreover, the thiophene alkylation was exothermic while the olefin oligomerization was endothermic. On the basis of these findings obtained by experimental and theoretical investigation, two methods that might be useful to further inhibit the occurrence of side reactions and improve the catalyst performance in the alkylation process were proposed.