Aerobic granular sludge was successfully cultivated with the effluent of internal circulation reactor in a pilot-scale sequencing batch reactor (SBR). Soy protein wastewater was used as an external carbon source for altering the influent chemical oxygen demand/nitrogen (COD/N) ratios of SBR. Initially, the phenomenon of partial nitrification was observed and depressed by increasing the influent COD/N ratios from 3.32 to 7.24 mg/mg. After 90 days of aerobic granulation, the mixed liquor suspended solids concentration of the reactor increased from 2.80 to 7.02 g/L, while the sludge volumetric index decreased from 105.51 to 42.99 mL/g. The diameters of mature aerobic granules vary in the range of 1.2 to 2.0 mm. The reactor showed excellent removal performances for COD and after aerobic granulation, and average removal efficiencies were over 93% and 98%, respectively. The result of this study could provide further information on the development of aerobic granule-based system for full-scale applications.