In this study, purification of the wastewater from corn stover-based bioethanol production process with simultaneous biogas production was investigated in a combined system, which was based on thermophilic anaerobic digestion in a fluidized bed reactor (AFBR), an aerobic airlift loop reactor (ALR), and a biological aerated filter (BAF). High strength distillery wastewater and high ammonia nitrogen content pretreatment wastewater were used as the influents. In the thermophilic anaerobic process (54-55°C), the methane yield of 280 ± 10.1 ml/g-COD removed was obtained at organic loading rate (OLR) of 14.1 ± 0.21 g-COD/l day and hydraulic retention time (HRT) of 48 h in the AFBR. Then co-digestion of anaerobic effluent and pretreatment wastewater was carried out in the ALR. COD and NH-N average removal rate of 88.5 ± 1.5% and 96.7 ± 1.2% were obtained at HRT of 10 h, temperature of 30-33°C and superficial gas velocity ( μ) of 12 mm/s. The aerobic effluent was finally purified in the BAF operated at ambient temperature and HRT of 5 h with simultaneous removal of COD, NH-N and chroma. Final effluent with COD and NH-N concentrations of 65.1 ± 5.1 mg/l and 3.9 ± 0.5 mg/l was obtained with other main indexes satisfying the primary discharge standards for the ethanol industry in China. [ABSTRACT FROM AUTHOR]