A series of copper complexes derived from salen ligands bis(salicylaldimine) (L1), bis(pyrrole-2-carboxaldimine) (L2) and bis(pyridine-2-carboxaldimine) (L3) have been synthesized and encapsulated into the supercage of zeolite. These complexes were well investigated by various spectrochemical and physicochemical techniques with DFT calculations. Both free and encapsulated complexes were applied as catalyst to the degradation of methylene blue (MB) using H2O2 as oxidant. The alternation of coordinated sites N2O2 with N4 causes the enhanced catalytic activity, which is attributed to the increased molecular planarity and lower oxidation states for the free complexes. Moreover, encapsulated complexes showed modified geometric, optical and catalytic properties due to electronic effects and steric constraints from the host zeolite supercage. The encapsulated complexes show high catalytic efficiency in organic dye degradation in a neutral condition compared to other encapsulated catalyst studied and show good resistance to radical scavenger. Encapsulated complexes CuL2-Y and CuL3-Y coordinated with N4 sites, exhibiting enhanced catalytic reactivity and recyclability compared to free complexes in solution, which is important for the design of heterogeneous catalyst. The encapsulated complexes with the highest energy electronic band are more reactive. The zeolite and electronic effects from different coordination sphere play an important role in the functionality of the modified geometries.