Metal single-atom alloys (SAAs) are important catalysts in many catalytic reactions, while the preparation of metal SAA catalysts is a major challenge because the metal species can inevitably deposit on both support and the host metal when using conventional preparation methods, leading to decreased catalytic performances. In this work, we report the preparation of metal SAA by the galvanic replacement (GR) to selectively deposit metal species on the host nanocrystals (NCs) prior to loading on a support. It includes the first synthesis of Ni NCs by colloidal method and the following deposition of Pd atoms onto Ni NCs via GR. After that, the Pd1Ni nanocrystal alloys were deposited onto SiO2 and the atomic intimacy of Pd with Ni was confirmed by multiple characterization techniques. The Pd1Ni/SiO2 SAA prepared by GR presented improved catalytic reactivity in semi-hydrogenation of acetylene, as compared to the reference PdNi/SiO2 catalyst prepared by impregnation. Moreover, the Pd1Ni/SiO2-GR catalyst showed higher C2H4 selectivity in a wide range of temperatures (30–180 °C), which was better than Pd1Ni/SiO2-I SAA, Pd/NiO-I and Pd/SiO2-I catalysts prepared by impregnation. The DFT explains the enhanced selectivity, which is due to the electron transfer from Ni nanocrystal to Pd single atoms. The electron transfer was resulted from the improved intimacy of Pd atoms and Ni nanocrystals.