Abstract: Membrane bioreactor (MBR) has been perceived as a new technique to treat domestic waste water in bench scale. To analyze the mechanism of sludge bulking process, the traditional biological method and modern quinone profiles technique were used to continuously monitor the change of microbial community structure and the micro-ecology succession in MBR. The results showed that the bacterial diversity index of active sludge in MBR was lower than other kinds of active sludge and the types of quinone were different from the others. In the bulking process of MBR the diversity quotient (DQ) and evenness quotient (EQ) of microbe decreased gradually. The DQ was stepped down from 10.90 to 7.12 and EQ stepped down from 0.84 to 0.51, which indicated that a converse succession happened. Through the analysis of different quinone composition by standard quinone sample, it was found that the sludge volume index (SVI) was increased gradually and the systemic removal efficiency of organic matter reduced, which was resulted from the filamentous bacteria growing. The dominant microbial population changed regularly in the filamentous bacterial bulking process, specifically the UQ-9 and MK-6 were dominant in filament bulking sludge.