The molecular basis for the high cis-alkene selectivity over intermetallic PtSn for alkyne semi-hydrogenation is demonstrated. Unlike the universal assumption that the bimetallic surface is saturated with atomic hydrogen, molecular hydrogen has a higher barrier for dissociative adsorption on intermetallic PtSn due to the deficiency of Pt three-fold sites. The resulting molecular behavior of adsorbed hydrogen on intermetallic PtSn nanoparticles leads to pairwise-hydrogenation of three alkynes to the corresponding cis-alkenes, satisfying both high stereoselectivity and high chemoselectivity.