The sequence batch reactor experiment is used to study the effects of copper, zinc and nickel on the apparent yield, bio-adsorption degradation capacity, flocculation and settling performance, oxygen consumption rate and other aspects at different ion concentrations. And under the situation of two heavy metal ions co-existence and when the dosing concentrations are different, the interaction between the heavy metal ions is tested. The results of the experiment showed that when the situation of two heavy metal ions co-existence, the total concentrations of Cu2+ and Zn2+, Cu2+ and Ni2+, Zn2+and Ni2+ are within 5,5, 10 mg/L respectively, it had a little influence on the apparent yield of sludge, the system can run stably；The total concentrations of Cu2+ and Zn2+, Cu2+ and Ni2+, Zn2+ and Ni2+ are within 5,3, 3 mg/L respectively, it had no effect on the removal rate of CODCr and MLSS can be increased stably. If the concentrations are larger than these points, the system can not run normally; When Cu2+ and Ni2+ coexist, there will be a synergistic inhibition on microbial respiration.