Intermetallic compounds (IMCs) have evoked considerable attention as high-selectivity catalysts in chemical processes by virtue of their exceptional structural properties. Here we report a general method to obtain Ni-based IMCs via structural transformation from layered double hydroxides (LDHs) precursor, which exhibit excellent selectivity toward CO hydrogenation in various unsaturated aldehydes (crotonaldehyde, 3-methyl-2-butenal, 2-pentenal, furfural, 5-hydroxymethylfurfural and cinnamaldehyde). The optimal catalyst (NiBi IMCs) displays surprisingly high selectivity toward unsaturated alcohols (97.2%, 93.2%, 94.5%, 97.7%, 97.9% and 98.9%, respectively). A combination investigation based on STEM, XANES, and in situ COIR verifies a rugged and ordered surface atomic structure, due to the huge difference in atomic radius between Ni and Bi. Both experiment characterization (in situ FT-IR) and theory calculation (DFT) reveal that the well-organized surface atomic arrangement with a steric hindering effect gives rise to the vertical adsorption configuration of unsaturated aldehydes, resulting in selective hydrogenation of CO instead of CC group. This work shows a significant paradigm for investigation of LDHs-based IMCs catalyst via a deep viewpoint on structure-selectivity relationship, which is potentially applied as a hopeful candidate in heterogeneous hydrogenation catalysis.