Two new copper(II) complexes, [Cu(benzim)2(bipy)(MeOH)](ClO4)(2) (Complex 1) and Cu(benzim)2(phen) (MeOH)](ClO4)(2) (Complex 2)] (bipy = 2,2'-bipyridine, phen = 1,10-phenanthroline and benzim = 1-benzyl-1Hbenzimidazole) have been synthesized and successfully characterized with single crystal x-ray diffraction analysis. Crystal structures of complexes revealed that both possess distorted square pyramidal geometries coordinated with a solvent molecule (CH3OH) at apical positions. The in vitro cytotoxicity of these Cu(II) complexes was carried out in HCC1428 and HUVEC cell lines. Molecular docking was also used to evaluate and understand the interaction modes of the complexes with the molecular target DNA and HSA (Human Serum Albumin). DNA binding capacities of complexes were analyzed by fluorescent titration method. Structural changes in the nucleus as a result of the effects of the complexes were discussed by viewing them with DAPI staining. Furthermore, biological activities of complexes and ligands were analyzed in silico. The cell lines IC50 results were obtained at similar rates (~8-fold) to the constant inhibition values obtained by docking studies. In addition, the fluorescence titration and circular dichrosim studies of the compounds with dsDNA-TO complexes showed results in agreement with docking studies. In our study, it was determined that phen ligand has a much more effective biological activity than bipy ligand in copper(II) complex synthesized with benzimidazole.