The electrochemical hydrogenation of HMF to BHMF is an elegant alternative to the conventional thermocatalytic route for the production of high-value-added chemicals from biomass resources. In virtue of the wide potential window with promising Faradic efficiency (FE) towards BHMF, Cu-based electrode has been in the center of investigation. However, its structure–activity relationship remains ambiguous and its intrinsic catalytic activity is still unsatisfactory. In this work, we develop a two-step oxidation–reduction strategy to reconstruct the surface atom arrangement of the Cu foam (CF). By combination of multiple quasi-situ/in-situ techniques and density functional theory (DFT) calculation, the critical factor that governs the reaction is demonstrated to be facet effect of the metallic Cu crystal: Cu(110) facet accounts for the most favorable surface with enhanced chemisorption with reactants and selective production of BHMF, while Cu(100) facet might trigger the accumulation of the by-product 5,5′-bis(hydroxymethy)hydrofurion (BHH). With the optimized composition of the facets on the reconstructed Cu(OH)₂-ER/CF, the performance could be noticeably enhanced with a BHMF FE of 92.3% and HMF conversion of 98.5% at a potential of −0.15 V versus reversible hydrogen electrode (vs. RHE) in 0.1 M KOH solution. This work sheds light on the incomplete mechanistic puzzle for Cu-catalyzed electrochemical hydrogenation of HMF to BHMF, and provides a theoretical foundation for further precise design of highly efficient catalytic electrodes.