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It is a challenge to selectively hydrogenate 4-nitrostyrene to 4-nitroethylbenzene, due to the similar energy barrier of hydrogenation of the nitro and vinyl groups. Herein, we demonstrate that such selective hydrogenation can be achieved by Pd@Ru core–shell nanocubes that are prepared by epitaxial growth of a face-centered cubic Ru shell on Pd cubes. The core–shell structure of Pd@Ru nanocubes is confirmed by transmission electron microscopy, X-ray diffraction spectroscopy, and elemental mapping measurements. It is found that the electronic structure and hence the catalytic activity of the Pd@Ru nanocubes can be readily modulated by the Ru shell thickness. This is manifested in electrochemical CO stripping measurements where a decrease of CO adsorption energy is observed on Pd@Ru nanocubes with the increase of the Ru shell thickness. Results from this study suggest that deliberate structural engineering can be exploited to prepare bimetallic core–shell nanostructures for highly active and selective hydrogenation of organic molecules with multifunctional moieties.