Triple negative breast cancer (TNBC) is the most malignant subtype of breast cancer in which the cell surface lacks usual targets for drug to exhibit its effects. Epirubicin (Epi) is widely used for TNBC, but a substantial number of patients develop Epi resistance that is usually associated with poor prognosis. Transforming growth factor (TGF-β) is a multifunctional cytokine. In recent study, it appears that TGF-β influences the cancer stem cell population, thus, the drug resistance of cancer may also be affected. We used epirubicin to treat MDA-MB-231 (MB-231) cells and found that TGF-β and breast cancer stem cell markers CD44+CD24− were increased and were dose-dependent of epirubicin. We established drug-resistant cell line from parental MB-231 cells by chronic treatment with low-concentration epirubicin. The MB-231/Epi cell line showed relatively slow growth rate with varied morphology. Transwell assay and drug sensitivity assay revealed that the malignant cell behaviors in terms of migration, invasion and epirubicin-resistant properties were markedly increased in the MB-231/Epi cells. Western blot, immunofluorescence assay, and flow cytometry were used to analyze the expression levels of the breast cancer stem cell markers, CD44 and CD24. Mammospheres assay showed that the stemness of MB-231/Epi was increased compared to their parental cells. Interestingly, MB-231/Epi cells showed different expression levels of apoptosis-related markers: Bcl2, Bax; EMT-related markers E-cadherin, N-cadherin and cell cycle-related marker cyclinD1. These genes have all been shown to be regulated by the TGF-β pathway. Taken together, our findings suggest that TGF-β plays a vital role in TNBC epirubicin-resistance through regulating stemness, EMT and apoptosis.