Mitochondrial adenosine triphosphate (ATP) synthase is the key enzyme of mitochondrial oxidative phosphorylation reaction.The down-regulation of the mitochondrial ATP synthase is a hallmark of most human carcinomas, which is the embodiment of the bioenergetic signature of cancer in the performance of the decreased oxidative phosphorylation and increased aerobic glycolysis. Combining with the bioenergetic signature of cancer, studies showed that mitochondrial ATP synthase and multidrug resistance and adverse prognosis of tumor were closely related. Its mechanisms are related to post-transcriptional regulation of the ATP synthase,the hypermethylation of the ATP synthase gene and the inhibitor peptide of the mitochondrial ATP synthase, called ATP synthase inhibitory factor 1(IF1). In this review, we stress the biological characteristics of mitochondrial ATP synthase and the relationship between ATP synthase and multidrug resistance and prognosis of Malignant tumor, in order to find a new way for tumor therapy.