The submerged membrane bioreactor is one of the recent technologies for domestic wastewater treatment. In this study, the performance of the pilot-scale submerged membrane bioreactor coupled with sequencing batch reactor (SM-SBR) was investigated. The reactor was operated in sequencing batch modes with a 3-hour cycles consisting of anoxic and aerobic conditions to treat organics, nitrogen and phosphorus. Despite large fluctuations in influent conditions, COD removal was found to be higher than 95%. Sufficient nitrification was obtained within a few weeks after start-up and during the stable period. Moreover, complete nitrification occurred despite of short aeration time. Total nitrogen (TN) removal efficiency was up to 85%. The insufficient organic loading caused by the membrane fouling led to the increase of HRT, leading to endogenous respiration and/or deactivation of nitrifying microorganisms. DGGE patterns confirmed the shift in microbial community structure. The ammonia-oxidizers (i.e. Nitrospira) became dominant in the mixed liquor during long-term operations. Nitrification and denitrification processes were greatly affected by the temperature, while organic removal and phosphorus removal efficiencies were relatively stable below 15°C.