Biological nutrient removal (BNR) is generally integrated in municipal wastewater treatment plants to alleviate the impact of treated effluent on receiving watersheds. This paper studies the performance of BNR in a membrane bioreactor system consisting of anaerobic, anoxic, micro-aerobic and aerobic compartments treating a synthetic wastewater containing low organic matters. The membrane bioreactor system designed an anti-stream, stepwise return flow scheme to produce ideal conditions for the occurrence of simultaneous nitrification and denitification and denitrifying phosphorus removal processes. The proposed membrane reactor system has established higher biomass concentrations and ideal environments for biological nutrient removal processes, which results in high nutrient removal efficiencies treating low organic wastewaters. Four compartment configurations in the reactor system minimized the impact of oxidized nitrogen species in return flow on phosphorus release in the anaerobic tank and the anti-stream, stepwise return flow scheme encouraged the utilization of nitrate as the electronic acceptor in phosphorus uptake in the micro-aerobic tank. Denitrifying phosphorus removal and simultaneous nitrification and denitrification processes are the main mechanisms responsible for efficient nutrient removal. High phosphorus release activities and high phosphate concentration in the anaerobic tank make it is potentially feasible to recover phosphorus resource from wastewater.