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Abstract Effective control on chemoselectivity in the catalytic hydrogenation of C=O over C=C bonds is uncommon with Pd‐based catalysts because of the favored adsorption of C=C bonds on Pd surface. Here we report a unique orthorhombic PdSn intermetallic phase with unprecedented chemoselectivity toward C=O hydrogenation. We observed the formation and metastability of this PdSn phase in situ. During a natural cooling process, the PdSn nanoparticles readily revert to the favored Pd₃Sn₂phase. Instead, using a thermal quenching method, we prepared a pure‐phase PdSn nanocatalyst. PdSn shows an >96 % selectivity toward hydrogenating C=O bonds of various α,β‐unsaturated aldehydes, highest in reported Pd‐based catalysts. Further study suggests that efficient quenching prevents the reversion from PdSn‐ to Pd₃Sn₂‐structured surface, the key to the desired catalytic performance. Density functional theory calculations and analysis of reaction kinetics provide an explanation for the observed high selectivity.