We examined expression differences in breast cancer stem cells (BCSCs) of the doxorubicin-resistant breast cancer cell line MCF-7/ADM and doxorubicin-sensitive cell line MCF-7/S. The effects of Chinese medicine β-elemene on BCSCs and resistance protein expression were determined. The serum-free cell culture method was used for cell culture, and morphology was observed to determine the rate of cell sphere formation. Reverse transcription-polymerase chain reaction was used to detect breast cancer resistance protein (BCRP) and P-glycoprotein (P-gp) gene expression. Flow cytometry was used to determine BCRP- and P-gp-positive cell rates and CD44 + CD24-/low cell ratios. Morphological observation and gene amplification showed that compared with MCF-7/S cells, the serum-free cell sphere-forming rate and P-gp and BCRP gene expression levels were higher in MCF-7/ADM cells. Flow cytometry results showed that P-gp and BCRP protein expression in MCF-7/ADM cells was 77.78 ± 9.55% and 32.33 ± 5.12%, respectively, and the CD44 + CD24-/low cell rate was 64.79 ± 11.78%, which were all significantly higher than those in MCF-7/S cells (3.97 ± 1.51, 14.26 ± 2.51, 18.79 ± 3.28%; P < 0.05). β-elemene significantly decreased the serum-free cell sphere-forming rate in MCF-7/ADM cells and BCRP and P-gp gene/protein expression (P < 0.01). The proportion of CD44 + CD24-/low cells was reduced. MCF-7/ADM highly expressed the drug-resistant proteins BCRP and P-gp, which can be used for long-term in vitro culture and as a seed cell for studies of BCSCs. β-elemene can inhibit BCSC and the sphere-forming rate in MCF-7/ADM cells and reduce BCRP expression.