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(V)=Oa], 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 (Ob, Oa, and H2O), the calculated results support that the bridge Ob 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 XO4(n-) can effectively tune the catalytic activity of polyoxometalates, in the order of Ge(IV) > Si(IV).