The effects of dopant on the photocatalytic activity of SrTiO3-based systems are investigated using first principle DFT calculations. The SrTiO3:Rh(1%) loaded with Pt has been found to give the best efficiency in water splitting; however the same host doped with Ru leads to very low H2 evolution rate even it has a better visible light response. The analysis of the density of state and the calculated absorption spectra were used to illustrate the mechanisms that influence the photocatalytic efficiency. Our calculation results suggested that the two competing factors ─ the free electron generation (via light harvesting) and the charge recombination (due to the presence of recombination centers) process ─ result in the existence of the optimal doping concentration for the transition-metal-doped SrTiO3 lattice. We also found that the energy states introduced by dopant Rh in the bandgap of SrTiO3 were very close to the valence band maximum. These new states thus reduce the bandgap of catalyst and enhance its light absorption capability. The study of dopant clustering showed that the proximity of these states to the valence band allows for efficient electron replenishment and makes them less possible to trap active electrons. In contrast, the energy states introduced by dopant Ru are significantly higher than the valence band, making them an isolated recombination center. These Ru associated states also reduces the driving force for oxidation reaction. As a result, the Rh-doped SrTiO3 catalysts are found to provide a high H2 evolution rate.