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In this research article, the synthesis, structural characterization, and biological, DNA binding and anticancer properties of pyrimidine incorporated Schiff base ligand L and its [CuL2](ClO4)2 (1) and [ZnL2](ClO4)2 (2) complexes are reported. The isolated complexes 1 and 2 have significant antibacterial and antifungal properties, greater than those of ligand L. The interaction between protein and L were analyzed by an in silico method. The intercalative binding of the prepared compounds was proved from electronic absorption, fluorometric, cyclic voltammetric and viscometric methods. The calculated binding parameters such as, Kb (2.65×103, L; 7.74×103, 1 and 2.99×103, 2); Ksv (3.30×103, L; 4.31×103, 1 and 3.89×103, 2), and Kapp (2.15×105, L; 3.30×105, 1 and 2.82×105, 2) indicted that complex 1 has better interaction ability than L and complex 2. The in vitro anticancer properties of L, and complexes 1 and 2 against human cancer (MCF-7, HeLa and HEp-2) and normal (NHDF) cell lines were determined by the MTT assay method. The obtained results designated that complexes 1 and 2 exhibited substantial anticancer activity against the cancer cell lines, better than that of L.