In this study, the effect on the stability of Aerobic Granular Sludge (AGS) caused by an AGS separator was investigated. The AGS separator was a hydrocyclone. The main factors of the AGS separator were filter pore size (0.125∼0.600 mm), conical-to-cylindrical ratio (1.5∼3.0), and operating time (1∼20 min). The AGS/mixed liquor suspended solid (MLSS) ratio gradually increased to 0.500 mm (AGS/MLSS: 84.3±3.0%). AGS was best separated at the conical-to-cylindrical ratio of 2.5 (AGS/MLSS: 84.7±3.3%). As the operating time increased, the AGS separation performance also tended to increase. The shortest AGS separator run time, but the highest AGS separation performance was 10 min (87.0±2.5%). AGS stability was evaluated by operating the selected AGS separator and sequencing batch reactor. The average removal efficiencies of TOC, TCODCr, SS, TN, and TP were 95.7%, 96.9%, 93.0%, 89.0%, and 96.2%, respectively, which met the effluent standards in Korea. In addition, the AGS/MLSS ratio tended to remain constant, and the sludge volume index demonstrated a tendency to decrease from 140 mL/g to 70 mL/g. During the operation, the particles of AGS in optical microscope observations gradually increased.