Non-alcoholic fatty liver disease (NAFLD) is a liver disease closely related to metabolic syndrome. Hepatic mitochondrial dysfunction, as one of the most important features of NAFLD, leads to simple liver steatosis or progresses to steatohepatitis, and even liver fibrosis, which may eventually induce cirrhosis and hepatocellular carcinoma. However, there is no specific drug for the treatment of NAFLD in clinic. Recent studies found that mitochondrial dysfunction is related to ultrastructural damage, mitochondrial DNA depletion, excessive production of reactive oxygen species, and abnormities of fatty acid oxidation, mitochondrial autophagy, apoptosis, signal transduction. This article reviewed the performance, role, and mechanism of mitochondrial dysfunction in the progression of NAFLD and discussed the therapeutic strategies of NAFLD based on the understanding of mitochondrial dysfunction in NAFLD, providing new ideas for the development of innovative drugs for the prevention and treatment of NAFLD.