Tannin extract desulfurization technology is widely applied in China, however, in which there are sulfur-containing byproducts that can cause negative effects, such as reducing desulfurization efficiency and increasing operating cost etc. Thus, inhibiting side reactions and controlling byproducts is an important problem to be resolved. In this article, the cause of byproducts formation by thermodynamic analysis is reported. First, the reaction mechanism between HS and pentavalent vanadium V(V) in desulfurization solution is researched, and it is conclude that HS can transforms instantly into polysulfide ions Sx 2, then Sx 2 forms the element sulfur. Thus, Sx 2 is the main source to generate byproducts. Second, by calculating and comparing the Gibbs free energy change of side reactions, the results show that Sx 2 is more active than HS in solution and can react more easily with oxygen to produce byproducts. Therefore, quickening the transformation from Sx 2 to element sulfur is a key measure to resolve the problem on side reaction.