A strategy for the synthesis of PtRh alloy 3D porous nanostructures by controlled aggregation of nanoparticles in oleylamine is presented. The atomic ratio between the two components (Pt and Rh) is tuned by varying the concentration of precursor salts accommodating the oxidation of methanol. The morphology of PtRh alloy nanostructure is controlled by elevating the temperature of the reaction system to 240 °C. The prepared 3D porous nanostructures provide a high degree of electrochemical activity and good durability toward the methanol oxidation reaction compared to those of the commercial Pt/C (E-TEK) and PtRh nanoparticles. Therefore, the 3D alloy porous nanostructures provide a good opportunity to explore their catalytic properties for methanol oxidation.