The performance of a real-time controlled Sequencing Batch Membrane Bioreactor (SBMBR) for removing organic matter and nitrogen from synthetic wastewater has been investigated in this study under two specific ammonia loadings of 0.0086 and 0.0045g NH4+-N gVSS−1 day−1. Laboratory results indicate that both COD and DOC removal are greater than 97.5% (w/w) but the major benefit of using membrane for solid-liquid separation is that the effluent can be decanted through the membrane while aeration is continued during the draw stage. With a continued aeration, the sludge cake layer is prevented from forming thus alleviating the membrane clogging problem in addition to significant nitrification activities observed in the draw stage. With adequate aeration in the oxic stage, the nitrogen removal efficiency exceeding 99% can be achieved with the SBMBR system. Furthermore, the SBMBR system has also been used to study the occurrence of ammonia valley and nitrate knee that can be used for real-time control of the biological process. Under appropriate ammonia loading rates, applicable ammonia valley and nitrate knee are detected. The real-time control of the SBMBR can be performed based on on-line ORP and pH measurements.