RY10-4, a novel protoapigenone analog with a specific nonaromatic B-ring, displayed enhanced cytotoxicity in various tumor cells, especially for breast cancer cells, but the underlying mechanism remains unclear. In the present study, we confirmed the pro-apoptotic effect of RY10-4 on breast cancer cells. Furthermore, mitochondrial calcium uniporter (MCU) was proved to be up-regulated in RY10-4-treated MDA-MB-231 cells, which resulted in the overload of mitochondrial calcium ([Ca2+]m) and subsequently disrupted mitochondrial functions (characterized by mitochondrial reactive oxygen species (mtROS) accumulation, membrane potential (Delta psi m) depolarization and permeability transition pore (mPTP) opening). And finally, the mitochondrial apoptosis was activated by the release of cytochrome C. Interestingly, knockdown of MCU attenuated the overload of [Ca2+]m and blocked the apoptosis of MDA-MB-231 cells induced by RY10-4, which was consistent with the in vivo results. Taken together, this study proved that RY10-4 could induce apoptosis of breast cancer cells by elevating [Ca2+]m through MCU. Our work contributed previously unknown insights into the mechanisms involving in the clinical efficacy of RY10-4 on breast cancer cells, which also advanced calcium homeostasis as a potential target for chemotherapeutic drugs.