Abstract: Protein stereochemical modification (SCM) is a unique type of low-abundance post-translational modification associated with many human diseases. Because it does not change the molecular weight of proteins, traditional proteomics methods are generally not suitable for their discovery and identification. As ions migrate differentially when they collide with the buffer gas in a drift tube, the ions can be separated according to their mass, shape and charge by ion mobility-mass spectrometry (IM-MS), thus providing a means of conformation-based separation, which enables fast identification and separation of protein SCM. In this review, from the perspective of native IM-MS, the performances of five commercial ion mobility analyzers were introduced and compared, including drift tube ion mobility spectrometer, traveling wave ion mobility spectrometer, differential mobility analyzer, high-field asymmetric waveform ion mobility spectrometer, and trapped ion mobility spectrometer. It was focused on the recent advances of the analysis and identification for protein SCM via native IM-MS, and the role of structural MS strategy in the study of SCM effect on ligand-receptor interactions, especially the application of collision-induced unfolding techniques to the conformational study of chirality-regulated neuropeptide-receptor complexes. Finally, the future directions of IM-MS-based SCM identification and quantification were discussed, and guidelines for the next phase study of protein SCM were offered.