Two isomeric Zinc (II) complexes constructed by 3,5‐bis(1‐imidazoly) pyridine has been synthesized and characterized by single crystal X‐ray diffraction, elemental analyses and infrared spectroscopy. The binding mode and ability of complex 1–2 with CT‐DNA were studied by UV and fluorescence spectra. The intrinsic binding constant Kb (Kb1 = 2.305 × 104 M−1, Kb2 = 3.095 × 104 M−1) and the observed association constant Kobs (Kobs1 = 1.523*106 M−1, Kobs2 = 2.057*106 M−1) indicated that the insertion ability of complex 2 with CT‐DNA is stronger than complex 1. Gel electrophoresis showed that complexes have a good ability to hydrolyze cleavage pBR322 plasmid DNA. The cytotoxicity and apoptosis studies showed that complexes exhibited excellent cytotoxic activity against HeLa cells, especially complex 2 had better growth inhibition than Cisplatin. Molecular docking study simulated the binding model of complexes with DNA (PDB:4av1), showing an imidazole plane of complex 2 can be inserted into a DNA base pair in relative parallel. Both complexes can be used as potential anticancer agents.