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Glioblastoma (GBM), one of the most malignant brain tumors in the world, has limited treatment options and a dismal survival rate. Effective and safe disease-modifying drugs for glioblastoma are urgently needed. Here, we identified a small molecule, Molephantin (EM-5), effectively penetrated the blood-brain barrier (BBB) and demonstrated notable antitumor effects against GBM with good safety profiles both in vitro and in vivo. Mechanistically, EM-5 not only inhibits the proliferation and invasion of GBM cells but also induces cell apoptosis through the reactive oxygen species (ROS)-mediated PI3K/Akt/mTOR pathway. Furthermore, EM-5 causes mitochondrial dysfunction and blocks mitophagy flux by impeding the fusion of mitophagosomes with lysosomes. It is noteworthy that EM-5 does not interfere with the initiation of autophagosome formation or lysosomal function. Additionally, the mitophagy flux blockage caused by EM-5 was driven by the accumulation of intracellular ROS. In vivo, EM-5 exhibited significant efficacy in suppressing tumor growth in a xenograft model. Collectively, our findings not only identified EM-5 as a promising, effective, and safe lead compound for treating GBM but also uncovered its underlying mechanisms from the perspective of apoptosis and mitophagy. • EM-5 with BBB permeability exerts profound inhibitory effects on tumor growth in GBM cells, both in vitro and in vivo. • EM-5 induces cell apoptosis via ROS-mediated PI3K/Akt/mTOR pathway. • EM-5 triggers mitochondrial damage, characterized by reduced MMP, mitochondrial dynamics imbalance, and OXPHOS dysfunction. • EM-5 impairs mitophagy by disrupting mitophagosome-lysosome fusion through ROS generation. [ABSTRACT FROM AUTHOR]