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The nutrient (nitrogen and phosphorus) removal from municipal wastewater was investigated by sequencing batch reactor (SBR) with different aeration rates. The results indicated that the removal performances of nitrogen and phosphorus both increased first and then decreased with increasing aeration rates, and that the aeration rate should be controlled at 25 L.h–1 (dissolved oxygen = 2.7 mg.L–1) in order to achieve ideal removal efficiencies of total nitrogen (TN) and total phosphorus (TP). Aeration rate had a prominent effect on the occurrence of nitrification and denitrification (SND), and excessive aeration would weaken nitrogen removal during SND process. In contrast, excessive aeration had no effect on the release rate of the anaerobic phosphorus, and the decrease of these polyhydroxyalkanoates (PHAs) could significantly influence phosphorus uptake, which was very essential for controlling the biological phosphate removal.