Ion mobility mass spectrometry (IM-MS) has been broadly utilized in the structural characterization of noncovalent, supramolecular complexes. In this chapter, we discuss three types of supramolecular complexes, and their structural dynamics observed in IM-MS studies. Firstly, host–guest chemistry of cucurbituril, crown ether, and cyclodextrin is discussed. Secondly, self-assembly mechanisms of amino acids and peptides are introduced. Finally, structural studies of protein–protein complexes are presented. We mainly focus on insights into the physicochemical properties of supramolecular complexes (e.g. molecular interactions, role of water molecules in complexation and structural features).