The occurrence of multidrug resistance (MDR) is highly associated with the overexpression of ATP-binding cassette (ABC) transporters, among which, P-glycoprotein (P-gp) plays one of the most important roles. Iso-pencillixanthone A (iso-PXA) is a compound isolated from the marine-derived fungus Penicillium oxalicum. No studies on the anti-tumor effect of this compound have been reported, except for a few focusing on its bactericidal properties. In this study, we found iso-PXA could stimulate P-gp ATPase activity and attenuate P-gp expression to increase the intracellular drug concentration in the cervical vincristine (VCR)-resistant cell line HeLa/VCR. Then, it increased ROS generation, depolarized MMP, promoted the release of cytochrome c from mitochondria, and further activated caspase-9, caspase-3 and PARP to induce cell apoptosis effectively through the intrinsic pathway. Caspase-8 medicated cleavage of Bid into the truncated form tBid partially initiated the mitochondrial apoptotic events. The elevation of the Bax/Bcl-2 ratio, the accumulation of FBW7 and the degradation of Mcl-1 accelerated the iso-PXA induced apoptotic process. The HeLa/VCR cell xenograft model again confirmed that iso-PXA had much better efficacy than vincristine in vivo. Taken together, these findings demonstrated that iso-PXA elicited remarkable anti-tumor and anti-MDR activity through inhibiting P-gp expression and function and re-activating the intrinsic apoptosis pathway in vitro and in vivo, suggesting it as a potential chemotherapeutic lead compound in the treatment of cervical MDR cancers.