To investigate the relationship between microbial properties and membrane fouling, an anoxic-aerobic membrane bioreactor (A/O-MBR) was established and run at room temperature. The techniques of Terminal Restriction Fragment Length Polymorphism (T-RFLP) and Atomic Force Microscope (AFM) were used for analyzing the role of microorganisms for membrane fouling in different stages, and the three-stage model was applied to study the development process of membrane fouling in a whole cycle. The results showed that the process of MBR membrane fouling could be divided into three stages. The solid or dissolved materials attached to the membrane wire surface and the membrane pore were the main reason for the lower flux. The microbial community structures were different and changed with the deepening membrane fouling in the Aerobic mixture, the Cake layer and the membrane wire surface. With the increasing of the membrane pressure, the succession of dominant populations of the microbial in the Cake layer is: Rhizobiales Bacterium →Burkholderia sp.→Uncultured Nitrospira sp.→Thiothrix Eikelboomii →ZoogloeaRamigera→ Betaproteobacterium, and ZoogloeaRamigera is greatly related to the viscous material on the surface of membrane.