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Multi-stage A/O-MBR processes were designed to improve wastewater treatment efficiency; three different designs were carried out and compared in this study. The 2(A/O)-MBR process, i.e., with two sets of anoxic/oxic tanks in series, showed better effluent quality than A/O-MBR and 3(A/O)-MBR processes. The removal rates of COD, NH<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msubsup><mrow></mrow><mn>4</mn><mo>+</mo></msubsup></mrow></semantics></math></inline-formula>-N, TP and TN were 95.29%, 89.47%, 83.55% and 78.58%, respectively, complying satisfactorily with China’s urban sewage treatment plant pollutant discharge standards. In terms of membrane fouling, the 3(A/O)-MBR process demonstrated the lowest fouling propensity. The microbial community structure in each bioreaction tank was analyzed, the results from which matched with the process efficiency and fouling behavior.