A series of Pd/BEA catalysts with various Pd loadings were synthesized. Two active Pd2+ species, Z−-Pd2+-Z− and Z−-Pd(OH)+, on exchanged sites of zeolites, were identified by in situ FTIR using CO and NH3 respectively. Higher NOx storage capacity of Z−-Pd2+-Z− was demonstrated compared with that of Z−-Pd(OH)+, which was caused by the different resistance to H2O. Besides, lower Pd loading led to a sharp decline of Z−-Pd(OH)+, which was attributed to the ‘exchange preference’ for Z−-Pd2+-Z− in BEA. Based on this research, the atom utilization of Pd can be improved by decreasing Pd loading.