Direct utilization of crude glycerol, a major byproduct in biodiesel industry, becomes imperative, because its production has outpaced the demand recently. We demonstrated that the oleaginous yeast Rhodosporidium toruloides Y4 had a great capacity to convert glycerol into lipids with high yield using the two-stage production process. Significantly higher cell mass and lipid yield were observed when the media were made with synthetic crude glycerol than pure glycerol. The process achieved a lipid yield of 0.22 g g−1 glycerol, which was comparable with the lipid yield using glucose as the substrate. Lipid samples showed similar fatty acid compositional profiles to those of vegetable oils, suggesting that such microbial lipids were potential feedstock for biodiesel production. Our data provided an attractive route to integrate biodiesel production with microbial lipid technology for better resource efficiency and economical viability.