The chemoselective hydrogenation of unsaturated carbonyl compounds is one of the most important and challenging chemical processes in the fine chemical synthesis field, where intermetallic compounds (IMCs) have attracted extensive interest as efficient catalysts. In this work, we demonstrate the preparation of several Ni–In IMCs (Ni3In, Ni2In, NiIn, and Ni2In3) with a tunable particle size via the utilization of layered double hydroxides (LDHs) precursors that exhibit largely enhanced catalytic activity and selectivity toward the hydrogenation of α,β-unsaturated aldehydes. H2-TPR and semi-in situ XRD measurements reveal a coreduction process in the topotactic transformation of NiIn-LDHs materials to Ni–In IMCs. The catalytic behavior toward various unsaturated carbonyl compounds (e.g., furfural, 1-phenyltanol, crotonaldehyde, and 2-hexenal) can be improved by the modulation of the Ni/In ratio and the particle size of these Ni–In IMCs. For instance, a yield of 99% for the hydrogenation of furfural to furfuryl alcohol was obtained over supported Ni2In catalyst (particle size 5.1 nm, 110 °C, 3 MP, 2 h). The XAFS characterization and DFT calculation further reveal the electron transfer and active-site isolation in Ni–In IMCs, accounting for the largely enhanced hydrogenation selectivity. The control over the activity and selectivity of Ni–In IMCs catalysts makes them promising candidates for the chemoselective hydrogenation of unsaturated carbonyl compounds.