Aerobic granules were cultivated in a sequencing batch reactor (SBR). COD and ammonia nitrogen removal rate were 94% and 99%, respectively. The diameter, settling velocity and SVI10 of granules ranged from 2 to 5 mm, 80 to 110 m/h and about 40 mL/g, respectively. Freezing microtome images, DO concentration profiles by microelectrode, distribution of bacteria and EPS by confocal laser scanning microscopy (CLSM) show that the aerobic granules have a three-layer structure. Each layer has different thickness, character, bacteria, and DO transfer rate. A hypothesis for granule structure is proposed: the first layer, the surface of the granule, is composed mostly of heterotrophic organisms for organic matter removal, with a thickness range from 150 to 350 μm; the second layer, mostly composed of autotrophic organisms for ammonia nitrogen removal, with a thickness range from 250 to 450 μm; the third layer, located in the core of the granule, has mostly an inorganic composition and contains pores and channels.