Cholestatic liver disease, caused by accumulation of hazardous bile acids in the liver, may result in cirrhosis, fibrosis, or liver failure. Activation of Sirt6 prevents cholestasis-associated pathological events such as oxidative stress and mitochondrial biogenesis disorders and inhibits bile acid synthesis to alleviate cholestatic liver injury. However, it is still uncertain which route is responsible for the therapeutic effect of Sirt6 in reducing cholestasis. For this reason, we administered liver-specific Sirt6 knockout mice with N-Acetylcysteine, Keap1-Nrf2-IN-1 or acadesine to remove oxidative stress and/or trigger mitochondrial biogenesis after cholestatic liver disease modeling, but these measures did not significantly improve cholestatic symptoms. Unlike the antioxidant or triggers of mitochondrial biogenesis, MDL801, a Sirt6 agonist suppressing CYP7A1 expression and down-regulating serum bile acid levels, exhibited favorable therapeutic effects. It suggests that inhibition of hepatic bile acid synthesis is the main pathway by which Sirt6 alleviates cholestatic liver disease. These findings provide a solid basis for the possible application of Sirt6 agonists in the treatment of cholestatic liver disease.