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Three new transition metal complexes, Cu(II) 1, Co(II) 2, and Zn(II) 3 with ligand “bimnap” derived from 1-methyl-2-aminobenzimidazole and 2-hydroxynapthaldehyde were synthesized and characterized. The structure of the ligand was determined by single X-ray crystallography. All the three complexes, 1–3, were examined for the mode of interaction with biomolecule viz., calf thymus-DNA (CT-DNA) using various spectroscopic methods. The nuclease activity was performed against pBR322 DNA that exhibited concentration-dependent degradation of the nucleic acid. The mechanism of DNA cleavage was studied by the electrophoretic pattern in the presence of the radical scavengers. Also, the complexes 1–3 were analyzed for groove binding affinity. Moreover, in vitro cytotoxicities of the complexes 1–3 were tested against the five human cancer cell lines, i.e., HeLa, SK-MEL-1, HepG2, HT108, and MDA-MB 231. Also, the cell adhesion and migration properties upon treatment of cell lines with complexes 1–3, and consequently, their cell death pathway via apoptosis and necrosis were analyzed. Further, complexes 1–3 were studied in vivo for their toxicities and tolerabilities in mice. In sum, the complexes 1–3 showed merits of an effective anticancer agent in cell lines–based study while minor side effects were observed in vivo.