Using spin-polarized density functional calculations, we investigate the role of different Pd/Pt ensembles in determining CO chemisorption on Au-based bimetallic alloys through a study of the energetics, charge transfer, geometric and electronic structures of CO on various Pd/Pt ensembles (monomer/dimer/trimer/tetramer). We find that the effect of Pd ensembles on the reduction of CO chemisorption energy is much larger than the Pt ensemble case. In particular, small-sized Pd ensembles like monomer show a substantial reduction of CO chemisorption energy compared to the pure Pd (111) surface, while there are no significant size and shape effects of Pt ensembles on CO chemisorption energy. This is related to two factors: (1) the steeper potential energy surface (PES) of CO in Pd (111) than in Pt (111), indicating that the effect of switch of binding site preference on CO chemisorption energy is much larger in Pd ensembles than in Pt ensembles, and (2) down-shift of d-band in Pd ensembles/up-shift of d-band in Pt ensembles as compared to the corresponding pure Pd (111)/Pt (111) surfaces, suggesting more reduced activity of Pd ensembles toward CO adsorption than the Pt ensemble case. We also present the different bonding mechanism of CO on Pd/Pt ensembles by the analysis of orbital resolved density of state.