Dye wastewater is one of typically non-biodegradable industrial effluents. A new process linking Fenton’s oxidation with biological oxidation proposed in this study was investigated to degrade the organic substances from real dye wastewater. During the combination process, the Fenton’s oxidation process can reduce the organic load and enhance biodegradability of dye wastewater, which is followed by biological aerated filter (BAF) system to further remove organic substances in terms of discharge requirement. The results showed that 97.6% of chemical oxygen demand (COD) removal by the combination process was achieved at the optimum process parameters: pH of 3.5, H2O2 of 2.0 mL/L, Fe(II) of 500 mg/L, 2.0 h treatment time in the Fenton’s oxidation process and hydraulic retention time (HRT) of 5 h in the BAF system. Under these conditions, COD concentration of effluent was 72.6 mg/L whereas 3020 mg/L in the influent, thus meeting the requirement of treated dye wastewater discharge performed by Chinese government (less than 100 mg/L). These results obtained here suggest that the new process combining Fenton’s oxidation with biological oxidation may provide an economical and effective alternative for treatment of non-biodegradable industrial wastewater.