BACKGROUND: This study aimed to explore the metabolic changes during neoadjuvant chemoradiotherapy (NCRT) in patients with locally advanced rectal cancer (LARC) by serum metabolomics analysis, and to provide new biomarkers for individualized treatment and efficacy prediction. METHODS: Serum samples from 20 patients with LARC before, during and after NCRT were collected for metabolomic analysis. The metabolites in the serum samples were analyzed qualitatively and quantitatively using gas chromatography-mass spectrometry (GC-MS). Meanwhile, the differences in metabolic profiles at different time points were compared and significantly changed metabolites were screened. RESULTS: The metabolic profiles of patients were significantly altered at different time points of NCRT. Through metabolomic analysis, we identified metabolites that were significantly altered during NCRT and revealed alterations in the associated metabolic pathways. The predictive power of pre-radiotherapy isocitric acid and pro-radiotherapy 3-hydroxy-3-(4'-hydroxy-3'-methoxyphenyl) propionic acid in distinguishing patients sensitive and non-sensitive to NCRT was markedly high, with AUC values of 0.875 and 0.75, respectively. Additional analysis indicated that a combined panel of serum metabolites yielded even higher AUC values, thereby enhancing the accuracy of predicting the efficacy of neoadjuvant NCRT. CONCLUSION: This study revealed metabolic changes and corresponding alterations in metabolic pathways during NCRT in patients with LARC by serum metabolomic analysis. The metabolic disorders may be associated with poor outcomes in patients treated with NCRT for rectal cancer, providing new biomarkers for individualized treatment and prognostic assessment. Further studies and validation will help to gain insight into the mechanism of these metabolic changes and provide more basis for clinical application.