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Breast cancer is a heterogeneous malignancy that often changes during diagnosis and treatment, so timely monitoring of tumors, patients and treatment responses is crucial to improve the prognosis of patients. With the development of precision oncology, early patient stratification and the formulation of tailored therapeutic approaches have become essential strategies to maximize treatment efficacy. Several techniques, such as molecular pathology and genomics analysis have been thoroughly studied in the diagnosis and treatment of breast cancer, but they only evaluate and analyze from the perspective of patients or tumors in isolation. Metabolomics uses high-throughput analytical techniques to provide a functional readout of the biological phenotype, reflecting the sum of alterations occurring at the DNA, RNA, and protein levels. Therefore, through the detection of tumor tissues and peripheral blood of patients, metabolomics could describe the bidirectional interaction between the tumor and its microenvironment, as well as the systemic metabolic changes in patients to evaluate cancer progression from both tumor and patient aspects in a more comprehensive way. In this review, we summarize the currently available techniques for metabolomics and how metabolomics can be used to improve the clinical management of breast cancer patients, including diagnosis, treatment, and prognosis. We also discuss current challenges and future directions in metabolomics research.