Cancer cells gain a growth advantage through the so-called Warburg effect by shifting glucose metabolism from oxidative phosphorylation to aerobic glycolysis. Hypoxia-inducible factor 1 (HIF-1) has been suggested to function in metabolic reprogramming; however, the underlying mechanism has not been fully elucidated. We found that the aberrant expression of wild-type isocitrate dehydrogenase 3 alpha (IDH3 alpha), a subunit of the IDH3 heterotetramer, decreased alpha-ketoglutarate levels and increased the stability and transactivation activity of HIF-1 alpha in cancer cells. The silencing of IDH3 alpha significantly delayed tumor growth by suppressing the HIF-1-mediated Warburg effect and angiogenesis. IDH3 alpha expression was associated with the poor postoperative overall survival of lung and breast cancer patients. These results justify the exploitation of IDH3 as a novel target for the diagnosis and treatment of cancers.