The search for non-noble metal catalysts for chemical transformations is of paramount importance. In this study, an efficient non-noble metal catalyst for hydrogenation, hexagonal close-packed cobalt (HCP-Co), was synthesized through a simple one-step reduction of β-Co(OH)2nanosheets via a temperature-induced phase transition. The obtained HCP-Co exhibited several-times-higher catalytic efficiency than its face-centered cubic cobalt (FCC-Co) counterpart in the hydrogenation of the C=C/C=O group, especially for the 5-hydroxymethylfurfural (HMF) hydrogenation (8.5-fold enhancement). Density functional theory calculations demonstrated that HMF molecules were adsorbed more firmly on the (112_0) facet of HCP-Co than that on the (111) facet of FCC-Co, favoring the activation of the C=O group in the HMF molecule. The stronger adsorption on the (112_0) facet of HCP-Co also led to lower activation energy than that on the (111) facet of FCC-Co, thereby resulting in high activity and selectivity. Moreover, HCP-Co exhibited outstanding catalytic stability during the hydrogenation of HMF. These results highlight the possibility of fabricating hydrogenation catalysts with satisfactory catalytic properties by precisely tuning their active crystal phase.