Removal of azo dye from wastewater with biological method is a complicated process, including decolorization and mineralization. However, there is little understanding of the functional microbial community involved in the whole dye degradation process. In this study, a simplified model using anaerobic3-oxic2-sedimentaion reactor was proposed. Acid Orange and Methyl Orange were treated as model azo dyes. In each compartment, the degradation intermediates of azo dyes were identified with UV–Vis, FTIR, HPLC-MS and GC-MS, and the corresponding microorganisms were determined with 16S rDNA high throughput Miseq sequencing. Decolorization happened in anaerobic compartments, while mineralization of the resulted aromatic amines mainly occurred under aerobic circumstance. LEfSe analysis demonstrated that the microbial community compositions were significantly influenced by the chemical structures of substrates. With t-value biplot, the relationship between azo dye degradation and microbial community structure was proposed statistically. It was found that the functional microbial communities varied with the change of azo dye degradation intermediates. Besides, cleavage of benzene ring also happened under anaerobic circumstance. This may be due to the genera of Parabacteroides and Bacteroides, which exhibited significantly positive relationships with 1,4-Benzenediol. With the new model, the performances and structures of functional microbial communities for NN- reduction and aromatic amines mineralization were characterized and the reaction mechanism was explored.