Pt nanoparticles encapsulated into zeolite Y (denoted as Pt@Y) exhibited approaching 100% catalytic selectivity to 2,5-bis-(hydroxymethyl)-furan (BHMF) at full conversion of 5-hydroxymethylfurfural (HMF) in the presence of H-2, coupled with good reusability. Zeolite Y constrained HMF to be adsorbed on encapsulated Pt nanoparticle surface via either the end of aldehyde groups or hydroxyl groups in thermodynamically unfavorable end-on mode to enlarge the gap in the activation energies between hydrogenation of aldehyde groups and hydrodehydroxylation of hydroxyl groups to favor selectivity enhancement via avoidance of further hydrodehydroxylation at moderate conditions, which provide a general method to avoid thermodynamics-regulated flat-lying conformation for simultaneous activation on the furan ring, aldehyde, and hydroxyl groups.