Alkaline pretreatment of straw materials prior to enzyme hydrolysis is a key step for bioconversion of lignocellulose to bioethanol and chemicals. Wastewater from the alkaline pretreatment process must be treated before discharge to minimize its environmental impact. In this study, biotreatment of the wastewater from soda-pretreatment process of corn stover was investigated using fungus Z-6, and some indexes such as color, chemical oxygen demand (COD), and lignin content of wastewater before and after biotreatment were determined to assess the effect of the biotreatment. Results showed that fungus treatment could remove color up to approximately 72% after 2 d, and decrease COD and lignin content by about 63% and 60%, respectively after 3 d. The wastewater was fractionated using dynamic ultrafiltration method, and the changes in lignin contents of the effluent fractions with different molecular weights before and after biotreatment were analyzed. Some compounds produced by the fungus during treatment were identified using gas chromatography-mass (GC-MS) spectrometer, which revealed that depolymerization of lignin occurred during the biotreatment process.