The removal efficiency of sequencing batch reactor (SBR) system with synthetic industrial estate wastewater (SIEWW) containing Ni 2+ or Pb 2+ was increased with the increase of mixed liquor suspended solids (MLSS). But, the sludge volume index (SVI) of the system was increased up to higher than 100 mL/g under MLSS of up to 4000 mg/L. Also, the effluent NO 3 − was decreased with the increase of MLSS. The heavy metals (Ni 2+ or Pb 2+), BOD 5, COD and TKN removal efficiencies of SBR system with SIEWW containing 5 mg/L heavy metal (Ni 2+ or Pb 2+) under MLSS of 3000 mg/L were 83–85%, 96–97%, 95–96% and 83–94%, respectively. The increase of heavy metal (Ni 2+ or Pb 2+) concentrations of SIEWW from 5 to 50 mg/L were not significantly effected to both COD and BOD 5 removal efficiencies (they were reduced by only 4–5%), but they were strongly effected to both TKN and heavy metals removal efficiencies (they were reduced by 15 and 20–30%, respectively). Both Ni 2+ and Pb 2+ could repress the growth of both nitrification and denitrification bacteria. And Ni 2+ was more effective than Pb 2+ to reduce the heavy metals removal efficiency. The SBR system could be applied to treat the industrial estate wastewater (IEWW) containing both Pb 2+ and Ni 2+ even the heavy metals concentrations was up to 5 mg/L, but the removal efficiency was quite low and excess bio-sludge did not produce. However, the system efficiency could be increased with the increase of BOD 5 concentration of the wastewater. The Pb 2+, Ni 2+, COD, BOD 5 and TKN removal efficiencies of the system with IEWW containing 500 mg/L BOD 5, 5 mg/L Ni 2+ and 5 mg/L Pb 2+ under HRT of 3 days were 85.68 ± 0.31%, 87.03 ± 0.21%, 86.0 ± 0.5%, 94.04 ± 0.4% and 90.5 ± 0.9%, respectively. And the effluent SRT, SS and SVI of the system were 44.7 ± 0.6 days, 150 ± 6 mg/L and 100 mL/g, respectively.