The research is to test the damage to DNA of effective microorganisms (EMs) by heavy metal ions As3+, Cd2+, Cr3+, Cu2+, Hg2+, Pb2+, and Zn2+, as well as the effects of EM bacteria on wastewater treatment capability when their DNA is damaged. The approach applied in this study is to test with COMET assay the damage of EM DNA in wastewater with different concentrations of heavy metal ions As3+, Cd2+, Cr3+, Cu2+, Hg2+, Pb2+, Zn2+, as well as the effects of EM treated with As3+, Cd2+, Cr3+, Cu2+, Hg2+, Pb2+, and Zn2+ on COD degrading capability in wastewater. The results showed that the damage of the DNA of EM were negatively correlated with their treatment capability and that EM bacteria maximum tolerant concentrations of these heavy metal ions was at 0.05 mg/L for As3+, 0.2 mg/L for Hg2+, 0.5 mg/L for Cd2+, Cr3+, and Cu2+, and 1 mg/L for Pb2+ and Zn2+.