Water oxidation is a key half reaction in the energy conversion scheme. The reaction mechanism for the oxidation of H₂O to O₂ catalyzed by single-Ru-substituted polyoxometalates, [Ru^III(H₂O)XW₁₁O₃₉]ⁿ⁻ (X = Si^IV, Ge^IV), was investigated by means of density functional calculations. The electronic structure of the pre-activation intermediates indicates that the aqua ligand is prone to accommodate the proton coupled electron transfer (PCET) process to achieve the active group [Ru^VO_a], and the high valent oxo-ruthenium(V) species are responsible for the O–O forming event. Three possible proton acceptors were designed for the rate-determining step (O_b, O_a, and H₂O), the calculated results support that the bridge O_b atom of the polytungstate ligand will act as the most favorable proton acceptor in the O–O bond formation, with an energy barrier of 28.43 kcal mol⁻¹. A detailed information of the peroxidic intermediates in the oxidation process was also characterized, both the peroxo-species [Ru^IV(OO)SiW₁₁O₃₉]⁶⁻ and [Ru^V(OO)SiW₁₁O₃₉]⁵⁻ show the six-coordinate isomer with an open terminal geometry is more favorable than the close seven-coordinate ones. In addition, the replacement of the heteroatom in XO₄ⁿ⁻ can effectively tune the catalytic activity of polyoxometalates, in the order of Ge^IV > Si^IV.