The present invention relates to a composition for effectively treating cancer stem cells, and more specifically to a composition for treating cancer stem cells, which contains a glucose uptake inhibitor, a biguanide-based compound, and a calcium pump inhibitor. The composition of the present invention can be used as an agent of treating cancer stem cells by effectively inducing apoptosis of the cancer stem cells. Accordingly, the composition of the present invention can be used as a pharmaceutical composition capable of effectively treating various cancer stem cells to effectively inhibiting cancer recurrence and/or metastasis.