Microbial lipid is a promising source of oil to produce biofuel if it can be generated from lignocellulosic materials. Mortierella isabellina is a filamentous fungal species featuring high content of oil in its cell biomass. In this work, M. isabellina was studied for lipid production from corn stover. The experimental results showed that M. isabellina could grow on different kinds of carbon sources including xylose and acetate, and the lipid content reached to 35 % at C/N ratio of 20. With dilution, M. isabellina could endure inhibition effects by dilute acid pretreatment of corn stover (0.3 g/L furfural, 1.2 g/L HMF, and 1 g/L 4-hydroxybenozic acid) and the strain formed pellets in the cell cultivations. An integrated process was developed combining the dilute acid pretreatment, cellulase hydrolysis, and cell cultivation for M. isabellina to convert corn stover to oil containing fungal biomass. With 7.5 % pretreated biomass solid loading ratio, the final lipid yield from sugar in pretreated biomass was 40 % and the final lipid concentration of the culture reached to 6.46 g/L.