Multiple sclerosis (MuS) is a chronic, inflammatory, demyelinating disease of the central nervous system, with a globally increasing prevalence. Its pathogenesis involves complex interactions among immune dysregulation, genetic predisposition, and environmental factors. These contribute to a wide spectrum of clinical manifestations, posing significant challenges for both diagnosis and treatment. Metabolomics, the comprehensive analysis of small-molecule metabolites, has emerged as a powerful approach to elucidate MuS pathophysiology and identify potential biomarkers. In particular, alterations in amino acid and lipid metabolism are closely associated with inflammation, myelin damage, neurotransmitter imbalance, and immune activation. This review summarizes recent advancements in the application of chromatography-mass spectrometry techniques to MuS biomarker research. Key technologies include liquid chromatography-tandem mass spectrometry (LC-MS/MS) for analyzing metabolites in biological fluids, high resolution mass spectrometry (HRMS) for precise metabolite identification, gas chromatography-mass spectrometry (GC-MS) for profiling volatile compounds, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for mapping spatial metabolite distributions in tissues. Metabolomic analyses of MuS patient samples have revealed significant disruptions in amino acid metabolism. For instance, reduced arginine levels and elevated asymmetric dimethylarginine levels in cerebrospinal fluid suggest vascular dysfunction. Altered tryptophan metabolism, including altered levels of kynurenic acid and 5-hydroxytryptophan, reflects neurotransmitter imbalances. Increased pyroglutamic acid levels indicate oxidative stress. Lipid metabolism is also markedly perturbed in MuS. Changes in palmitic acid levels affect cell membrane integrity, while alterations in sphingolipids, key components of myelin, are linked to demyelination. Elevated oxysterols correlate with neuroinflammation and immune dysregulation. Additionally, systemic lipid changes, such as reduced low-density lipoprotein and altered high-density lipoprotein cholesterol levels, have been associated with disease activity and progression. Due to their high sensitivity, resolution, and throughput, chromatography-mass spectrometry techniques are well-suited for detecting these metabolic alterations. Representative studies demonstrate the utility of LC-MS/MS in detecting amino acid perturbations in plasma and cerebrospinal fluid (CSF), GC-MS in identifying lipid abnormalities in serum, HRMS in generating detailed brain tissue metabolite profiles, and MALDI-TOF MS in visualizing lesion-specific metabolic distributions. These findings have led to the identification of promising biomarker candidates. For instance, decreased arginine may indicate endothelial dysfunction, while elevated oxysterols may serve as markers of neuroinflammatory activity. Such biomarkers hold potential for facilitating early diagnosis, disease monitoring, and personalized treatment strategies. Metabolomics via chromatography-mass spectrometry technologies has significantly advanced our understanding of MuS pathophysiology. Amino acid dysregulation affects neurotransmitter synthesis and immune modulation, while lipid imbalances impair myelin integrity and cellular signaling. These insights provide a foundation for the development of metabolite-based diagnostic tools and therapeutic interventions. Nonetheless, several challenges remain. MuS exhibits high heterogeneity, and metabolomic data are complex and variable. Improved biomarker specificity and standardization are needed for clinical application. Technological advances in chromatography-mass spectrometry resolution, along with standardized protocols, will be essential. Large-scale clinical validation across MuS subtypes is also critical. Integrating metabolomics with genomics and environmental factors may enhance biomarker reliability and elucidate individual disease trajectories. In conclusion, this review highlights the crucial role of chromatography-mass spectrometry-based metabolomics in MuS research. By unraveling the metabolic underpinnings of inflammation and demyelination, it provides valuable insights into disease mechanisms and introduces novel avenues for early diagnosis and targeted therapy. Collaborative research efforts and methodological rigor will be key to translating these discoveries into clinical impact.