The surface structure of supporting materials has great effect on the catalytic performance of supported catalysts. In this work, three kinds of Ru nanocrystals with different morphologies and surface structures, namely triangular plates (TPs), capped columns (CCs) and nanospheres (NSs), were used as substrates for the deposition of Pt particles through an aqueous adsorption–reduction approach. By testing the catalytic activity and stability of these composite catalysts towards methanol electrooxidation, the relationship between the surface structure of Ru nanocrystals and the catalytic performances of Pt particles was built up. Pt/Ru TPs/C exhibited higher catalytic activity and stability than Pt/Ru CCs/C, indicating that the closest packed facet of Ru serves as better substrate for the deposition of Pt particles than the high index facets of Ru for methanol electrooxidation. Pt particles and Ru NSs formed a self-supported network structure in Pt/Ru NSs/C, which increased the level of dispersion of Pt particles and guaranteed higher catalytic activity and stability compared with Pt/Ru CCs/C. This work demonstrated how to use shape controlled metal nanocrystals to study the surface structure effect of supports in catalytic reactions.