Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver metabolic syndrome which affects millions of people worldwide. Recently, improving mitochondrial function and autophagic ability have been proposed as a means to prevent NAFLD. It has been previously described that high-temperature requirement protein A2 (HtrA2/Omi) favors mitochondrial homeostasis and autophagy in hepatocytes. Thus, we explored the effects of HtrA2/Omi on regulating mitochondrial function and autophagy during NAFLD development. High-fat diet (HFD)-induced NAFLD in mice and free fatty acids (FFAs)-induced hepatocytes steatosis in vitro were established. Adeno-associated viruses (AAV) in vivo and plasmid in vitro were used to restore HtrA2/Omi expression. In this study, we reported that HtrA2/Omi expression considerably decreased in liver tissues from the HFD-induced NAFLD model and in L02 cells with FFA-treated. However, restoring HtrA2/Omi ameliorated hepatic steatosis, confirming by improved serum lipid profiles, glucose homeostasis, insulin resistance, histopathological lipid accumulation, and the gene expression related to lipid metabolism. Moreover, HtrA2/Omi also attenuated HFD-mediated mitochondrial dysfunction and autophagic blockage. TEM analysis revealed that liver mitochondrial structure and autophagosome formation were improved in hepatic HtrA2/Omi administration mice compared to HFD mice. And hepatic HtrA2/Omi overexpression enhanced mitochondrial fatty acid β-oxidation gene expression, elevated LC3II protein levels, induced LC3 puncta, and decreased SQSTM1/p62 protein levels. Furthermore, hepatic HtrA2/Omi increased respiratory exchange ratio and heat production in mice. Finally, HtrA2/Omi overexpression by plasmid significantly diminished lipid accumulation, mitochondrial dysfunction, and autophagic inhibition in FFA-treated L02 hepatocytes. Taken together, we demonstrated that HtrA2/Omi was a potential candidate for the treatment of NAFLD via improving mitochondrial functions, as well as restoring autophagic flux.