In this work, three supported Co-Sn intermetallic compound (IMC) catalysts (Co2.9Sn2, CoSn and CoSn2) with a particle size of similar to 20 nm were prepared via a facile hydrotalcite approach, and their catalytic performances were evaluated in the selective hydrogenation of citral to unsaturated alcohols (geraniol and nerol). EXAFS, in situ CO-FTIR and DFT calculation results reveal that the introduction of Sn in Co-Sn IMCs dramatically optimizes the geometric and electronic structures of active Co, in which Sn isolates the Co active-site and electron transfer occurs from Sn to the Co atom. H-2-TPD measurements indicate the presence of four different Co sites (labeled as alpha, beta, gamma and sigma) on the surface of these IMCs; the sample of CoSn IMC shows the largest beta/(gamma + sigma) ratio, which results in the highest selectivity toward unsaturated alcohols (SUA: 67.6%). DFT studies prove that the geometric and electronic effects of the CoSn IMC weaken the hydrogenation of the C=C group, accounting for the largely enhanced hydrogenation selectivity of citral to unsaturated alcohols.