Huntington’s disease (HD) is an inherited neurodegenerative disorder caused by an abnormal polyglutamine (polyQ) expansion in the protein Huntingtin (Htt). Currently, no cure is available for HD. The mechanisms by which mutant Htt causes neuronal dysfunction and degeneration remain to be fully elucidated. Nevertheless, mitochondrial dysfunction has been suggested as a key event mediating mutant Htt-induced neurotoxicity since neurons are energy-demanding and particularly susceptible to energy deficits and oxidative stress. SIRT3, a member of sirtuin family, is localized to mitochondria and has been implicated in energy metabolism. Notably, we found that cells expressing mutant Htt displayed reduced SIRT3 levels. Trans-(-)-ε-viniferin (viniferin), a natural product among our 22 collected naturally-occurring and semisynthetic stilbenic compounds, significantly attenuated mutant Htt-induced depletion of SIRT3, and protected cells from mutant Htt. We demonstrate that viniferin decreases levels of reactive oxygen species (ROS) and prevents loss of mitochondrial membrane potential in cells expressing mutant Htt. Expression of mutant Htt results in decreased deacetylase activity of SIRT3, and further leads to reduction in cellular NAD+ levels and mitochondrial biogenesis in cells. Viniferin activates AMPK and enhances mitochondrial biogenesis. Knockdown of SIRT3 significantly inhibited viniferin-mediated AMPK activation and diminished the neuroprotective effects of viniferin, suggesting that SIRT3 mediates the neuroprotection of viniferin. In conclusion, we establish a novel role for mitochondrial SIRT3 in HD pathogenesis, and discovered a natural product that has potent neuroprotection in HD models. Our results suggest that increasing mitochondrial SIRT3 might be considered as a new therapeutic approach to counteract HD, as well as other neurodegenerative diseases with similar mechanisms.