To valorize oleaginous Schizochytrium sp. biomass, a novel sequential process was addressed and developed to simultaneously produce high value DHA-enriched glycerides and low value bulky biodiesels. In this process, Schizochytrium sp. biomass was first treated by alkaline protease; then the resulting biomass was directly subjected to enzymatic ethanolysis catalyzed by liquid enzymes from C. antarctica (CALA), T. lanuginosus (TL), R. miehei (RM) and A. oryzae (PLA). For all four liquid lipases, the alkaline protease treatment on Schizochytrium sp. biomass significantly enhanced total lipid recovery, biodiesel yield and yield of DHA-enriched glycerides. Under optimized conditions, CALA and TL achieved the highest biodiesel yields 76.28-76.66 wt% based on microalgae TFAs while PLA had the lowest (55.25 wt%). Moreover, CALA attained the highest DHA (77.93 wt%) and LC PUFAs (93.08 wt%) contents in glyceride fraction, suggesting a superior performance to concentrate DHA and LC PUFAs in glycerides. C-13 NMR analysis illustrated that non-regiospecificity and unfavorability towards LC PUFAs of CALA made it possible to transesterify saturated fatty acids located in all 3 positions of microalgal oil; thus LC PUFAs were highly enriched in glycerides. Overall, the sequential process using enzymes and ethanol as green media was successfully established for the co-production of high-value microalgal bioproducts rich in LC PUFAs and sustainable biodiesels in a comprehensive manner.