We developed a comprehensive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the simultaneous analysis of 19 glycosaminoglycan disaccharide components. Although structural similarity among components can hinder MS identification, we optimized the LC conditions to successfully separate all components. Specifically, we quantitatively and qualitatively evaluated chondroitin sulfate (CS) and hyaluronic acid (HA) in food ingredients. The method involves enzymatic degradation of CS and HA by Chondroitinase ABC into their constituent disaccharides, followed by LC-MS/MS quantification. We identified conditions that ensure optimal enzymatic digestion of CS and HA. Calibration curves showed excellent precision, accuracy, and linearity in validation tests. Quantitative analyses of CS and HA in commercially available raw materials were consistent with labeled purity. Disaccharide composition analysis suggested that the origin stated on the label was accurate. The findings suggest that the proposed method is useful for the quantitative and qualitative evaluation of the functional food ingredients CS and HA.