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Compared to general cancer cells, cancer stem cells are stronger and more difficult to be killed by drugs. Therefore, traditional treatment methods have low efficacy according to cancer stem cells. In essence, one of the main causes of cancer survival, proliferation, transfer, and recurrence is the presence of cancer stem cells. In recent years, a large number of studies have demonstrated that natural plant products have powerful in killing cancer cells and have various structures, which possess low toxicity, multi-target regulation advantages in inducing cancer stem cells to apoptosis. Therefore, this provides new ideas for developing anti-cancer drugs by inducing cancer stem cell apoptosis by natural plant products. In this article, we will introduce the apoptotic mechanism of tumor stem cells, the importance of eliminating tumor stem cells, and the benefits of natural plant products in cancer treatment. In addition, this paper reviewed nine categories of chemicals in natural plant products that induce apoptosis of tumor stem cells and their mechanisms of action. We also summarized the mechanism of natural plant products inducing apoptosis of tumor stem cells. This review provides an important reference for the personalized treatment of cancer.