Aerobic granular sludge (AGS) was cultivated successfully in a sequencing batch reactor (SBR), which has floc sludge as seeding sludge in synthetic wastewater. Removal efficiency in the reactor during the entire working period was investigated. Controlling strategy for filamentous bulking and the effect of a filamentous microorganism on granulation of sludge were discussed. The results showed that whether filamentous bulking occurred or not, there was little impact on the removal rate of phosphorus and ammonia nitrogen, which maintain about 90% and 95%, respectively. Increasing the hydrodynamic shear force has certain effects on the controlling of filamentous bulking. Declining C/N ratio, balancing nutrition in feed water can fundamentally solve the problem of filamentous bulking in the cultivation process of aerobic granular sludge.