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Lipids represent an important class of biomolecules, and play numerous roles in physiological and pathological processes and activates. The enormous chemical and compositional diversity of lipids presents a significant challenge for lipidomics. The emerging technology of ion mobility-mass spectrometry (IM-MS) has provided an orthogonal separation to effectively improve resolving power and selectivity in lipid analysis. Meanwhile, IM-MS has also provided a valuable physiochemical property, namely, collision cross section (CCS), to facilitate lipid identification. In this review, we introduced the use of IM-MS technology to separate different lipid species and isomers. Then, we highlighted the applications of IM-MS for lipid structural identification in lipidomics. Finally, we discussed the potentials of IM-MS for the measurement and annotation of novel lipid species in biological samples.