The types of interactions between six novel bisnaphthalimide derivatives (AITHN, BITHN, PITHN, PyITHN, DN6 and DNT6) and calf thymus DNA in a physiological buffer (Tris-HCl buffer solutions, pH=7.4) were investigated using UV-vis spectrophotometry, fluorescence spectroscopy, and a competition experiment, in order to explore the relationships between the linkers of bisnaphthalimide derivatives and their activity. The absorption spectra of the six bisnaphthalimide derivatives with DNA showed a slight red shift and hypochromic effect. DNA quenched the compounds (AITHN, PITHN, PyITHN and DN6) by a static quenching process. Using acridine orange (AO) dye as a fluorescence probe, fluorescence quenching of the emission peak was observed in the AO-DNA system with the addition of PITHN, but the maximum emission intensity was elevated for AITHN and DN6 while the other three compounds showed no obvious change. The calculated binding constants of AITHN, PITHN, PyITHN and DN6 with DNA were 2.09×105Lmol-1, 1.14×105Lmol-1, 0.95×105Lmol-1 and 2.39×105Lmol-1 respectively, and the number of binding sites were 0.618, 0.323, 0.297 and 0.769. Intercalative and electrostatic binding were the two major modes between the six bisnaphthalimide derivatives and calf thymus DNA. The strength of the intercalation was related to the type of linker. Moreover, DN6 and AITHN had the greatest intercalative ability. The electrostatic binding ability of the six compounds was independent of the type of linker present.