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[Display omitted] • The furfural hydrogenation mechanisms are systematically investigated in vapor phase and aqueous phase. • A proton-shuttling mechanism in aqueous phase is proposed. • The presence of water enhances the stability and activity of reaction intermediates. • The dynamic charge separation between the catalyst and the intermediates results in low hydrogenation barriers. The catalytic hydrogenation of biomass-derived compounds in the aqueous phase is crucial to upgrading renewable biochemicals and biofuels. Herein, by combining density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations, we have explored the selective hydrogenation mechanism of furfural on the copper surface with a fully explicit solvation model. The presence of water solvent could significantly affect the reaction mechanism, in adjunct with the charge interactions between the reaction intermediates and the Cu surface. It demonstrates a proton-shuttling mechanism for furfural hydrogenation where the initial hydrogen source for reducing the carbonyl group is from the dissociation of the adjacent water. Furthermore, the water solvation effect results in the dynamic charge separation between the copper surface and the reaction intermediates, significantly reducing the energy barrier. These results deepen our mechanistic understanding of selective hydrogenation of furfural over Cu-catalysts, paving the way for upgrading renewable biomass derivatives in applications. [ABSTRACT FROM AUTHOR]