An improved lipid extraction process has been established for microalgal using enzyme-assisted aqueous extraction processing (EAEP), which mainly involved in sonication and enzyme treatment. As compared to cellulase, neutral protease and alkaline protease, significantly higher lipid recovery was achieved by snailase and trypsin. The highest lipid recovery of 49.82% was obtained by a combined sonication-enzyme treatment at pH 4. The enhancement mechanism of the EAEP was analyzed in terms of the particle size of cream and zeta potential. In addition, microalgal lipid recovery was also affected by lipid class composition and the type of algae. The present study demonstrates a promising alternative to conventional lipid extraction of microalgae and the quantitative information on EAEP of oleaginous alga can provide valuable data for process design at pilot and industrial scale.