The position and cis-trans configuration of C═C bonds in unsaturated lipids significantly affect their biological activities. Simultaneous identification of the position and cis-trans configuration of C═C bonds in unsaturated lipids is important; nonetheless, it still remains a challenging task. Herein, a stereoselective asymmetric reaction was used to recognize cis-trans isomers of the C═C bonds, and the derivatized precursor ions and product ions were subjected to tandem ion mobility-mass spectrometry (IM-MS) analysis. The theoretical calculation revealed that the formation of intramolecular hydrogen bonds after the cyclization reaction amplified the structural difference between diastereomers and increased the separation efficiency in IM. Consequently, a simple, sensitive, and highly selective platform for simultaneous determination of the position and cis-trans configuration of various C═C bonds in unsaturated lipids was established. It was then successfully applied to pinpoint the cis-trans geometry conversion of the located C═C bonds in lipids of the bacterial membrane under environmental stress and track the heterogeneous distribution of unsaturated lipids in rats after spinal cord injury. The present study also offers new insights into the application of IM-MS technology in resolving molecular structures and demonstrates the potential as a platform for a broad range of applications.