In this work, two Cu(II) complexes containing 5-amino-1-R-1H-benzimidazol-4-yl)(4-chloro)phenylmethanone hydrazones ligands were synthesized and their spectral characterization, DFT calculations, and catalytic activity were reported. New heterocyclic hydrazone ligands were prepared by the reaction of o-amino-ketones with hydrazine hydrate in high yield. Structural assignments of new compounds were based on their microanalytical and spectral data and formula [Cu(L)2(H2O)2](SO4) was suggested for complexes. Moreover, to gain a further insight into the geometry of synthesized complexes, the DFT calculations were carried out at the B3LYP/6-311+G(d,p) level of theory. The catalytic activity of Cu(II) complexes as heterogeneous catalysts were also investigated in the synthesis of biologically active compound 3,4-dihydropyrimidin-2(1H)-one C5 ester, via classical Biginelli reaction followed by trans-esterification reaction. The results confirmed that the current method formed the products at the lower reaction time and high yields, which might as a result of the enhanced reactivity of the reactants on the surface sites of Cu(II) complexes.