Electrode catalysts composed of carbon supported PtRu nanoparticles (PtRu/C) synthesized by radiochemical process were annealed to control the PtRu substructure to enhance catalytic activity. The substructure of the PtRu nanoparticles synthesized by using high-energy electron beam under acidic condition was Pt-rich core/Ru-rich shell type, reflecting the redox potentials of each precursor ions. The material characterization techniques revealed that the reductive annealing led to the mixing of PtRu both in the core and on the surface. The sample with annealing temperature of 300 o C for 5 hour showed the highest methanol oxidation current, 2.3 times higher than that obtained with before annealing.