The oxidation process by molybdenum-containing enzyme, xanthine oxidase, is theoretically studied with a model complex representing the reaction center and a typical benchmark substrate, formamide. Comparisons were systematically made among reaction mechanisms proposed previously. In the concerted and stepwise mechanisms that were theoretically discussed previously, the oxidation reaction takes place with a moderate activation barrier. However, the product is less stable than the reactant complex, which indicates that these mechanisms are unlikely. Moreover, the product of the concerted mechanism is not consistent with the isotope experimental result. In addition to those mechanisms, another mechanism initiated by the deprotonation of the active site was newly investigated here. In the transition state of this reaction, the carbon atom of formamide interacts with the oxo ligand of the Mo center and the hydrogen atom is moving from the carbon atom to the thioxo ligand. This reaction takes place with a moderate activation barrier and considerably large exothermicity. Furthermore, the product by this mechanism is consistent with the isotope experimental result. Also, our computations clearly show that the deprotonation of the active site occurs with considerable exothermicity in the presence of glutamic acid and substrate. The intermediate of the stepwise mechanism could not be optimized in the case of the deprotonated active site. From all these results, it should be concluded that the one-step mechanism with the deprotonated active site is the most plausible.