In this study, the granular sludge was operated under low aeration condition in sequencing batch reactor (SBR) and advanced continuous flow reactor (ACFR), respectively. Through increasing the sludge retention time (SRT) from 22 days to 33 days, the ACFR was successful startup in 30 days and achieved long term stable operation. Under SBR operation condition, the aerobic granular sludge (AGS) showed good nitrogen (60%), phosphorus (96%) and COD removal performance. During stable operation of continuous-flow, the nitrogen removal efficiency was increasing to 70%, however, the phosphorus removal efficiency could only be restored to 65%. Meanwhile, the sludge discharge volume from ACFR was about half of that in SBR. Results of high-throughput pyrosequencing illustrated that methanogenic archaea (MA), ammonia oxidizing archaea (AOA), denitrifying bacteria (DNB), denitrifying polyphosphate-accumulating organisms (DPAOs) played an important role in the removal of nutrients in ACFR. This study could have positive effect on the practical application of AGS continuous flow process for simultaneous biological nutrient removal (SBNR).