Nano-sized PtRu catalysts supported on carbon nanoparticles were synthesized by a polyol process. The PtRu catalyst prepared at pH=3 indicated higher catalysis for methanol oxidation than one prepared at pH=5.5. The samples were analyzed by techniques of the extended X-ray absorption fine structure (EXAFS), transmission electron microscope (TEM), X-ray diffraction (XRD) and X-ray fluorescence (XRF). Their results showed that the pH of the precursor solution during the polyol process affected the substructure of the PtRu nanoparticles. The correlation of the substructure with the catalytic activity was studied.