This study investigates how the nucleation sequences of Pt and Ru crystallites affect the structure evolutions along with the methanol electrooxidation activity of bimetallic PtRu nanoparticles (BiNPs). We found that the BiNPs crystallites would transform from cubic to tetrakaidecahedron crystals on increasing the Ru content from 0 to 54 at%. This reduces the particle size and the size distributions during the nucleation-growth of the crystal. In the meantime, the unfilled d state and the heteroatomic intermixing of Pt atoms along with the MOR reactivity of the BiNPs will be enhanced. By increasing Ru >54 at%, the BiNPs would transform into an ellipsoid-like crystallite with a Ru rich core. This is because the Pt anions would replace the metallic Ru atoms and form a discrete sub-nano Pt nuclei at the NPs surface. Consequently, the surface MOR activity of the BiNPs is substantially suppressed.