In this study, an anaerobic baffled reactor (ABR) with four compartments was employed to treat alkali-decrement wastewater of polyester fabrics under different organic loading rates. The stable operation of this reactor was achieved in 70 days at a hydraulic retention time of 36 h and mesophilic temperature of 35 ± 1 °C. It is found that the chemical oxygen demand removal and decolorization of this system can be as high as 79.0% and 87.7%, respectively. The different acidogenesis and methanogenesis in four compartments was acclimated by the variation of pH, oxidation reduction potential values and operational conditions in the spatial distribution of the first to fourth compartments of the ABR system. In addition, the dehydrogenase activity (DHA) and coenzyme F420 concentrations along the four compartments ranged from 67.8 to 185.21 μgTF/(gVSS·h) (TF: triphenyl formazan; VSS: volatile suspended solids) and 0.123 to 0.411 μmol/g, respectively. These results indicated that the ABR could separate acidogenesis and methanogenesis in longitudinal distribution and treat well the alkali-decrement wastewater.