Ion chromatography is a technique commonly used to separate strongly polar and ionizable substances; it can be used to separate, identify, and quantify ionizable compounds in complex samples when coupled with mass spectrometry, and is currently being used in the application of food analysis, drug analysis, metabolomics and clinical poisoning analysis. Herein, we review the development of ion chromatography-mass spectrometry (IC-MS), its progress over the past 20 years, and future trends in the abovementioned areas. The IC-MS research progress and applications for the determination of inorganic anions, organic acids, polar pesticides, biogenic amines, and sugars in the food field are discussed. Drug analysis applications are discussed mainly in relation to the analysis of drug impurities, identifying drug degradation products, and determination of plasma concentration, while the separation and analysis of strongly polar metabolites, such as organic acids, sugar phosphates, and nucleotides in biological matrices are discussed in relation to metabolomics. Advances in the analysis of strongly polar or ionizable toxic compounds, such as alkyl methylphosphonic acid, methylphosphonic acid, glyphosate, 3-nitropropionic acid, and indandione rodenticides, are mainly discussed in clinical poisoning analysis field. This paper is expected to become a useful reference for the further expansion and application of IC-MS in the life and health fields.