Magnetic Resonance Spectroscopy (MRS), as a non-invasive molecular imaging technique, enables the quantitative detection of changes in cerebral metabolites, providing crucial insights into the pathophysiology, early diagnosis, and therapeutic monitoring of neurodegenerative diseases. This review summarizes the applications of MRS in Alzheimer’s disease (AD), Parkinson’s disease (PD), multiple sclerosis (MS), and type 2 diabetes-related cognitive impairment. Studies have shown that MRS can detect early abnormalities in neurotransmitter metabolism in the hippocampus in AD; reveal fluctuations in gamma-aminobutyric acid (GABA) levels and their response to dopamine therapy in PD; identify energy metabolic alterations associated with fatigue severity in MS; and demonstrate associations between prefrontal metabolites and glycemic control in cognitive impairment related to type 2 diabetes. Although currently limited by issues such as low sensitivity and complex signal interpretation, advances in high-field technology, ultra-fast sequences, and multimodal integration suggest broad prospects for MRS in the precise diagnosis and dynamic monitoring of neurodegenerative diseases.