Aiming at the membrane fouling problem produced during MBR working process, different controlling operations were used on two sets of parallel A／O-MBR systems (R1 and R2). The changing situation of the microbial community structure during the membrane pollution process was analyzed by T-RFLP method, and the microbial metabolites were quantified. The results show that under the different operational conditions, the dominant microbial species of Cake layer in R1 system (controlling method: temperature is 30 ℃; SRT is 60 days; Flux is 9.09 L／(m²·h); DO is 4 mg／L) is Oribacterium, Cytophaga sp., Anaeromyxobacter, Paracoccus, bp180 and Comamonadaceae, respectively. The membrane fouling cycle of R1 reactor is 30 days. The dominant microbial species of Cake layer in R2 system (controlling method: temperature is 20 ℃; SRT is 30 days; Flux is 13.42 L/（m²·h); DO is 2 mg／L) is Anaeromyxobacter, Oribacterium, Saprospiraceae and Myxobacterium, respectively. The dominant microbial species of membrane wire in R1 is Saprospiraceae, Nitrospira, Thiothrix sp. and bp92, respectively. The dominant microbial species of membrane wire in R2 is Thiothrix Eikelboomii, γ-Proteobacterium, Nitrospira, Thiothrix sp. and bp52, respectively. The membrane fouling cycle of R2 reactor is 11 days. The different running methods on A／O-MBR systems have a significant influence on the succession of microbial community. The ascending of microbial diversity Shannon index H of Cake layer and membrane wire may accelerate the membrane fouling process. The obvious increasing trend of microbial metabolites(EPS,SMP) content results in the membrane pollution getting worse. EPS of the Cake layer has a dominant contributive effect on the process of membrane fouling.