Microalgal lipids have been recognized as one of the crucial sources of liquid biofuels. In this review, composition and structure of microalgal lipids (lipidomics) have been reviewed. Lipidomics can play an essential role in liquid biofuel production via providing accurate structure information about microalgal lipids such as position of double bonds, length of carbon chains, and hetero-atom distribution. The total content (similar to 5-50 wt.%) of microalgal lipids can be determined by gravimetric methods (mainly direct organic solvent extraction) and spectrometry. There are mainly eight categories of lipids including fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, prenol lipids, saccharolipids, and polyketides. A scheme of isolation and structure analysis of microalgal lipids has been advised based on organic solvent extraction, saponification, and silica gel column chromatography. All carbon chains in these categories can be used in the production of alternative liquid biofuels with the necessary catalytic processes. Additionally, chlorophylls in microalgae also have an apparent effect on the characterization analysis of microalgal lipids and the application of lipids in catalytic conversion process. Therefore, the basic concept of microalgal lipids and how to determine their content in cells are firstly introduced in this review. Then, the detailed isolation procedure and structure information have been reviewed to guide the practical application of liquid biofuel production. Finally, the conclusions and future research suggestions have been recommended. This review provides the necessary guide for high-efficiency and low-cost cultivation of microalgae as via selected microalgae species with high content of lipids.