Minimizing the detrimental impacts of perfluorooctanoic acid (PFOA) on human health is a daunting task. Here, we aimed to propose effective strategies for reducing PFOA-induced mitochondrial toxicity in human liver and intestinal cells. PFOA could occupy the fatty acid-binding pockets of human peroxisome proliferator-activated receptor alpha (hPPARα). PFOA not only could structurally interact with hPPARα, but also substantially upregulated the expression levels of PPARα and its downstream gene (i.e., pyruvate dehydrogenase kinase (PDK4)). The increased expression of PDK4 was associated with the mitochondrial toxicity of PFOA, and inhibition of PDK4 or knock-down of PDK4 could effectively attenuate the mitochondrial toxicity of PFOA. Moreover, modification of carboxyl group via an esterification of PFOA into methyl perfluorooctanoate (MePFOA) decreased the affinity to hPPARα, resulting in the loss of upregulated expressions of PPARα and PDK4. Lower mitochondrial toxicity and cytotoxicity were found in the MePFOA-treated cells compared to PFOA exposure. Our study supported that the carboxyl group of PFOA (as functional head group) was required for inducing its mitochondrial toxicity. Two strategies, including modification of functional head group and inhibition of toxic target of PFOA, are feasible to ameliorate mitochondrial toxicity of PFOA.