This work systematically examines the influence of preparation methods on the active Cu+ anchoring sites over FAU zeolites and their CO storage capacity and selectivity. The involved preparation methods here include individual liquid ion exchange method with CuCl2 solution, individual solid ion exchange method with CuCl powder and the hybrid exchange method. For the obtained Cu-Y samples, XRD, Ar adsorption/desorption at 87 K, TEM and NMR were used to characterize their skeleton structure, meanwhile, XPS and H2-TPR were utilized to identify the Cu+, Cu2+ and CuCl distribution. The CO storage capacity was implemented through CO adsorption–desorption isotherms. The correlation between various Cu species and CO storage capacity was analyzed and DFT calculation was employed to further elucidate the optimal Cu+ location induced by preparation methods. Finally, it is found that the isolated Cu+ is the dominating CO adsorption sites and Cu+ on site III present higher bonding energy with CO molecules. The hybrid preparation method seems the optimal choice for Cu-Y synthesis since the initial liquid ion exchange operation could prevent the framework corrosion from the subsequent solid ion exchange process, which benefits the optimal CO storage capacity and CO/N2 selectivity.