The preferential oxidation (PROX) of CO is a promising strategy for trace CO clean up in H2-rich stream to fuel cells. In the present study, a series of TiO2 supported clusters were prepared and studied for the PROX of CO. Amongst, Ru/TiO2 catalyst exhibited remarkably high PROX activity in the operation temperature range of fuel cells. The effects of catalyst preparation and pre-treatment on the catalytic performance of Ru/TiO2 were investigated in detail. Ru/TiO2 catalyst prepared by photo-deposition and pre-treated under H2–CO atmosphere was found to be the most promising one and complete CO oxidation could be achieved at >373K. Ru/TiO2 pre-treated under different reducing atmospheres were characterized by high-resolution transmission electron microscopy (HRTEM), X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR) of CO adsorption. The surface reconstruction of Ru sites during catalyst pre-treatment was observed and isolated metallic Ru species was identified as preferred active sites for PROX reaction. Based on the catalytic and characterization results, the possible mechanism for PROX of CO over Ru/TiO2 was proposed.