Sweet medicines are a relatively untapped source of new drugs. Their biological activities are closely correlated to their chemical characteristics. However, accurately defining the chemical characteristics of glycans is a challenge due to their chemical heterogeneity and diversity. Gas chromatography-mass spectrometry (GC-MS) is an excellent technique for the analysis of glycans even though the preparation of adequate derivatives is necessary. We reviewed and discussed the most important methodologies currently used for glycan analysis in sweet medicines based on GC-MS, including the derivatization for monosaccharide analysis, hydrolysis methods for polysaccharide analysis, glycosidic linkage analysis based on methylation, and pyrolysis gas chromatography in carbohydrate analysis. Finally a strategy for quality control of sweet medicines based on quantification analysis is proposed.