We demonstrated that the reactivity, electrochemically active area (ECSA), and long-term structural stability of Pt-based core–shell nanoparticles (NPs) under the methanol oxidation reaction (MOR) can be controlled by the crystal structure and the chemical composition of the core. This approach is inspired by the structural relaxation of shell Pt atoms on two types of crystalline cores (e.g., Ru and Co) due to the differences in surface free energy between facets. Due to the isotropic facet energy of the Co cores, the initial formation of the Pt shell is under kinetic control when the shell thickness is less than two atomic layers (∼3 Å). After the surface layer is formed, the subsequent growth of the Pt shell atoms is under surface diffusion control. For Ru core crystallites with significantly different facet energies, the NPs are disk-like shaped, indicating that the shell atoms preferentially deposit onto the radial edges in the absence of nucleation barriers. In this case, the ECSA of the Rucore–Ptshell NPs is 2.23-fold higher than that of the Cocore–Ptshell NPs, which is promising in the electrocatalytic oxidation of methanol and H2O2 for the applications of fuel cells and sensors, respectively.