This article presents systematic investigations on the relationship between the catalytic property and the surface ligand density/core size of thiolate ligand-capped Pd nanoparticles (PdNPs). The systematic variations in the two-phase synthesis of PdNPs generated from sodium S-dodecylthiosulfate were performed. The resulting PdNPs were characterized by transmission electron microscopy (TEM), thermogravimetric analysis (TGA), and H-1 NMR and UV-vis spectroscopy. The decrease in the molar equivalent of sodium S-dodecylthiosulfate (Bunte salts) resulted in the formation of nanoparticles with lower surface ligand density and larger particle core size. A decrease in the molar equivalent of tetra-n-octylammonium bromide or an increase in reaction temperature generated nanoparticles with higher surface ligand density and smaller particle core size. As the molar equivalent of NaBH4 decreased, the particle core size increased. The catalysis studies on various PdNPs with different surface ligand density and average core size showed a strong correlation between the PdNP composition and the turnover frequency (TOF) of the isomerization of ally, alcohol. Optimized "good" PdNPs with lower surface ligand coverage and larger core size catalyzed the isomerization of various allyl alcohols to carbonyl analogues with high activity and selectivity.