Phosphomolybdic acid (H3PMo12O40, PMo12) was employed to modify PtRu nanocatalysts for methanol electro-oxidation. The results show that the performance of PtRu catalysts was improved by the formation of the negatively charged self-assembled PMo12 monolayer on the catalyst surface. Electrochemical measurements indicate that the PMo12-modified PtRu catalyst has a higher catalytic activity and a better poison tolerance than the unmodified one. It is also found that the sequence in which PtRu and PMo12 were deposited onto the carbon support during the preparation process has a major influence on the performance of PMo12-modified PtRu nanocatalysts. X-ray photoelectron spectra results show that the self-assembled PMo12 layer inhibits the formation of metal oxides/hydroxides on the surface of PtRu nanoparticles to some extent.