A copper(II) complex of 2,2′-(((methylenebis(oxy))bis(2,1-phenylene))-bis(azanylylidene))bis(methanylylidene)) diphenol (H2L) was encapsulated in the supercages of zeolite NaY by the flexible ligand method. The resulting product was characterized by physicochemical and spectroscopic methods. The encapsulated complex and its corresponding free complex were used as catalysts for the synthesis of benzimidazoles. The results showed that the catalytic activity and stability of the complex were both increased by encapsulation. The effects of amount of catalyst, solvent, leaching and reusability of the heterogeneous catalyst were investigated.