1, 8-(3, 6, 9-Trioxaundecane-1, 11-diyldioxy)xanthone (L), and its new Cu (II) complex [Cu.L.(CH3CN)2](ClO4)2 have been synthesized and characterized by 1H NMR, electrospray mass spectra (ESI-MS), elemental analyses, infrared spectra (IR) and X-ray single crystal diffraction. The crystal structure of complex shows that Cu (II) ion is encapsulated within the macrocycle of L. The geometry around copper is a distorted square bipyramid with two acetonitrile molecules at axial position, and four macrocyclic oxygens including the carbonyl oxygen on the equatorial positions. The interaction of Cu (II) complex with calf thymus DNA (ct DNA) has been investigated by spectrophotometric titrations, ethidium bromide (EB) displacement experiments, circular dichroism (CD) spectra and viscosity measurements. Results indicate that Cu (II) complex can intercalate into the DNA base pairs by the plane of xanthone ring. Furthermore, the Cu (II) complex was tested against tumor cell lines including ECA109, SGC7901 and GLC-82 by MTT (microculture tetrazolium) method. The studies of DNA-binding agree with the effects on the inhibition of tumor cells in vitro.