Aerobic granules were cultivated successively in column sequencing batch reactor (SBR) with the glucose as carbon source. The effect of copper (II) on the characteristics of aerobic granules was studied. Results showed that the physical, morphology and extracellular polymeric substances (EPS) of aerobic granules were influenced in different degree under different concentrations of copper (II) in sequencing batch reactor (SBR). The appropriate Cu2+ can be adsorbed by the microorganisms in aerobic granules under the functions of chelation and displacement of heavy metals. Under the Cu2+ concentration of 0.5～3.0mg/L, the stable MLSS and better settleable granules with higher S.G. and lower SVI can been attained in the reactors. The sludge can maintain the granules in stable till the Cu2+ concentration increases to 20.0mg/L. The ratios of EPSC/EPN distribute in 6.60～7.01 steadily under the Cu2+ concentration of 0.5～10.0mg/L.However, excess Cu2+ can destroy the metabolism balance of the microorganisms and the protein synthesization and genetic information transportation are baffled. When the Cu2+ concentration increase to 50mg/L, more filamentous appears in the granules and the compact granules change to in disperse. The ratios of EPSC/EPN evidently rise to 7.59 and 7.46 respectively under high Cu2+ concentration of 20.0mg/L and 50.0mg/L. It suggests that the microorganisms try to excreting more EPS and protecting itself from the environmental change.