An eco-friendly two-step synthetic method for synthesizing Pd@PdPt/CNTs nanoparticles was introduced and studied for the methanol oxidation reaction. The Pd@PdPt alloy core-shell structure was synthesized by preparing a surfactant-free monodispersed Pd/CNTs precursor through the hydrolysis of tetrachloropalladate (II) ion ([PdCl4]2−) in the presence of carbon nanotubes (CNTs) and the subsequent hydrogen reduction and followed by a galvanic replacement reaction. This method opens up an eco-friendly, practical, and straightforward route for synthesizing monometallic or bimetallic nanoparticles with a clean surfactant-free electrocatalytic surface. It is quite promising for large-scale preparation. The Pd@PdPt/CNTs electrocatalyst demonstrated a high specific mass activity for methanol oxidation (400.2 mAmgPt−1) and excellent stability towards direct methanol oxidation compared to its monometallic counterparts.