In this study, a lab-scale anaerobic/anoxic/zeolite biofilter-membrane bioreactor (A1/A2/ZB-MBR) was designed to treat coking wastewater. The 454 pyrosequencing was used to obtain the composition and dynamics of microbial community about the treatment system. The results showed that the system yielded stable effluent chemical oxidation demand (158.5 ± 21.8 mg/L) and ammonia (8.56 ± 7.30 mg/L), but fluctuant total nitrogen (31.4-165.1 mg/L) concentrations. In addition, 66,256 16S rRNA gene sequences were obtained from A2 and ZB-MBR, and the microbial diversity and richness for five samples were determined. Although community compositions in the five samples were quite different, bacteria assigned to phylum Proteobacteria and class Flavobacteria commonly existed and dominated the microbial populations. The pyrosequencing analysis revealed that the microbial community shifted in the ZB-MBR with the presence of zeolite. Some taxa began to appear in ZB-MBR and contributed to the system performance. Additionally, Nitrosomonas and Nitrobacter gradually became the dominant ammonia-oxidizing bacteria and nitrite-oxidizing bacteria during the operation, respectively, which are favorable for the stabilized ammonia removal. Our results proved that the ZB-MBR is an alternative technique for treating coking wastewater.