Glioblastoma (GBM) remains a lethal brain tumor with poor prognosis and limited therapeutic efficacy from temozolomide (TMZ) treatment. Prodigiosin (PG), a bioactive secondary metabolite, has demonstrated anti-tumor activity across a broad spectrum of tumors. This study aims to investigate the therapeutic potential and mechanism of PG combined with TMZ in treating GBM. The results demonstrated that the combination of PG and TMZ synergistically inhibited GBM cell proliferation, triggered apoptosis, and suppressed migration and invasion. Transcriptomic analysis revealed downregulation of focal adhesion and related signaling pathways. Functionally, the combination therapy reduced focal adhesion numbers and AKT phosphorylation. Co-treatment with PG and TMZ impaired autophagic flux, evidenced by LC3-II and p62 accumulation. Furthermore, the anti-proliferative effect and the accumulation of LC3-II and P62 by the combination therapy were enhanced by the autophagy inhibitor chloroquine (CQ) but not reversed by the autophagy activator rapamycin (Rapa), confirming autophagy inhibition as a key mechanism. In conclusion, PG sensitized GBM cells to TMZ by impairing autophagy and focal adhesion signaling, providing a preclinical rationale for the combinatorial strategy.