Microbial lipid and bio-ethanol were co-generated by an integrated process using corn cob bagasse as raw material. After pretreatment, the acid hydrolysate was used as substrate for microbial lipid fermentation, while the solid residue was further enzymatic hydrolysis for bio-ethanol production. The effect of acid loading and pretreatment time on microbial lipid and ethanol production were evaluated. Under the optimized condition for ethanol production, ~131.3g of ethanol and ~11.5g of microbial lipid were co-generated from 1kg raw material. On this condition, ~71.6% of the overall fermentable sugars in corn cob bagasse could be converted into valuable products. At the same time, at least 33% of the initial COD in the acid hydrolysate was depredated.