A new 3-methylpyridyl pendant-arms Cu(II)-Zn(II) hetero-binuclear complex was synthesized by condensation reaction of 3,3′-((ethane-1,2-diylbis((pyridin-2-ylmethyl)azanediyl))bis(methylene))bis(2-hydroxy-5-methylbenzaldehyde) (H2L) and propane diamine in the presence of metal ions. The structure was characterized by IR spectroscopy, UV-Vis spectroscopy, ES-MS spectroscopy and X-ray single-crystal diffraction. The crystal structure reveals that the complex crystallizes in hexagonal, space group P63/m, with a=1.982 18(17) nm, b=1.982 18(17) nm and c=1.839 4(2) nm. The coordination environment of Zn(II) and Cu(II) in complex can be described as approximately square pyramid, where the apical positions are occupied by acetate radical. Two metal centers are equivalently bridged by the phenolic oxygens and an acetate radical with the intermetallic separation of 0.289 7 nm. The interaction between the complex and calf thymus DNA (CT-DNA) was measured by cyclic voltammetry and viscosity studies, which shows a weak binding activity of 6.92×103mol/L.