Abstract: Breast cancer is a malignant tumor that predominantly affects women. The incidence of breast cancer has risen annually and is increasingly occurring in younger population, posing a significant threat to women’s health. Estrogen receptor-positive breast cancer is the most prevalent subtype, accounting for 75% of all cases. Endocrine therapy, particularly with tamoxifen, serves as the primary treatment for these subtypes. However, due to the highly heterogeneous nature of breast cancer, some patients remain at risk for recurrence even after undergoing tamoxifen treatment. Therefore, it is essential to investigate the mechanism of tamoxifen in breast cancer treatment from a single-cell perspective. In comparison to single-cell genomics and single-cell proteomics, single-cell metabolomics can offer a clearer representation of the chemical changes occurring within individual cells by measuring the end products of cellular activity—metabolites. Thus, this approach can provide a more direct reflection of the differences between cells. In this study, single-cell mass cytometry was employed to investigate metabolite alterations in MCF-7 cells upon exposure to tamoxifen, aiming to elucidate its mechanism from a single-cell perspective. The 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay was utilized to assess the impact of tamoxifen on MCF-7 cell proliferation and established optimal conditions for subsequent therapies involving these cells. The results showed that 576 metabolites under positive ion mode and 480 metabolites under negative ion mode are identified by using single-cell mass cytometry approach. In total, 811 metabolites are detected in MCF-7 cells without tamoxifen treatment compared to 776 metabolites identified following tamoxifen administration. It demonstrated that metabolites observed under negative ion mode effectively distinguish between MCF-7 cells treated with and without tamoxifen. Exposure to tamoxifen can result in upregulation of 28 metabolites and downregulation of 59 metabolites, and these changes predominantly influence metabolic pathways including taurine-hypotaurine metabolism, caffeine metabolism, cysteine-methionine metabolism, glycine-serine-threonine metabolism, purine metabolism, starch-sucrose metabolism, and pyrimidine metabolism. The findings indicated that the intervention of the aforementioned metabolites and metabolic pathways may represent one of the mechanisms through which tamoxifen exerts its effects against estrogen receptor-positive breast cancer. This study employed single-cell metabolomics based on mass spectrometry to explore the metabolic alterations in breast cancer cells induced by tamoxifen, which is often overlooked in metabolomics studies based on bulk cells. Furthermore, it elucidates the mechanism of tamoxifen’s action against estrogen receptor-positive breast cancer from a single-cell metabolomic perspective, thereby provides valuable insights for understanding the mechanisms underlying other therapeutic agents.