The surface structure-controlled synthesis of noble metal nanocrystals (NCs) bounded by high-index facets has become a hot research topic due to their potential to significantly improve catalytic performance. This study reports the preparation of monodisperse Au–Pd alloy NCs with systematic shape evolution from rhombic dodecahedral (RD) to trisoctahedral (TOH), and hexoctahedral (HOH) structures by varying the concentration of surfactant in the surfactant-mediated synthesis. The as-prepared three kinds of alloy NCs possess almost the same size and composition as each other. It is suggested that the surfactant containing long-chain octadecyltrimethyl ammonium (OTA+) ions plays a key role in the formation of high index facets, and the crystal growth kinetics may also have an effect on the formation of different nanocrystal morphologies. In addition, the catalytic activities of these NCs are evaluated by structure-sensitive reactions, including ethanol electro-oxidation and the catalytic reduction of 4-nitrophenol (4-NPh). These three types of Au–Pd alloy NCs exhibit different catalytic selectivities towards these two reactions. The catalytic activities toward electro-oxidation of ethanol are in the order of HOH > RD > TOH, which follows the order of their corresponding surface energies. However, the activities toward catalytic reduction of 4-NPh are in the order of RD > TOH > HOH, which should be related to the local structure of the surfaces.