Abstract: Cancer stem cells (CSCs) are a group of tumor cells with the potential for self-replication, multicellular differentiation, and therapeutic resistance-factors which contribute to tumor recurrence, distant metastasis, and the failure of tumor treatment. Mitochondrial homeostasis plays a key role in stemness maintenance and differentiation regulation of CSCs. Mitophagy or selective autophagy of mitochondria, is an important regulatory mechanism for the maintenance of mitochondrial homeostasis. However, the role of mitophagy in CSCs is controversial. Considering that mitophagy regulates mitochondrial quality control, it was originally thought to positively regulate tumor suppression and maintain intracellular homeostasis. However, in recent years, mitophagy has been reported to be involved in reducing oxidative stress damage of tumor cells and promoting tumor progression. Further research on the mechanism of mitophagy regulation can reveal new therapeutic targets for tumor treatment. In this review, we have focused on the role of mitophagy in stemness maintenance, metabolic transformation, and therapeutic resistance of CSCs.