Selective hydrogenation of dienes and trienes is an important process in pharmaceutical and chemical industries. Our group previously reported that the thiosulfate protocol using sodium S-alkylthiosulfate ligand could generate catalytically active Pd nanoparticles (PdNP) capped with lower density of alkanethiolate ligands. PdNP catalyst offers several advantages such as less metal-ligand dissociation and easier separation and recycling over transition metal complexes. Herein, the investigation of PdNP capped with octanethiolate ligands (C8 PdNP) for selective hydrogenation of conjugated dienes into monoenes and trienes into dienes is reported. The mechanistic studies suggest two major routes for the conjugated diene hydrogenation, 1,2-addition and 1,4-addition of hydrogen. The selectivity for two mono-hydrogenation products is controlled by the steric effect and thermodynamic stability of substrates. The successful application of C8 PdNP for selective hydrogenation of carbonyl conjugated allenes (cumulated dienes) is also presented. Hydrogenation of the nonconjuated C=C bond results in the formation of conjugated carbonyl products.