[Objective] The aim was to establish a convenient and effective method to evaluate the toxicity of heavy metal ions by using small molecular DNA. [Method] pUC18 DNA which had exposed to the four heavy metal ions of Hg2+, Cr6+, Pb2+, Cd2+ was used to study the bioactivity of DNA; simultaneously, gel electrophoresis and hyperchromic effect were employed to detect the mechanism of DNA damage. [Result] The bioactivity of the exposed DNA was decreased and the influence degree was Hg2+Cr6+Pb2+Cd2+; the gel electrophoresis and hyperchromic effect proved that the main reason leading to reduce the bioactivity was DNA cross link, in the order pf Hg2+Cr6+Pb2+Cd2+. [Conclusion] The study indicated that pUC18 DNA could be used to assay the damage of DNA causing by heavy mental ions, which may be a potential, simple and effective tool to evaluate toxicity of heavy metal ions to DNA.