Non-alcoholic fatty liver disease (NAFLD) is a clinical pathological syndrome characterized by excessive fat deposition in liver cells, posing a new challenge in the field of contemporary medicine. Schisandrin A (SchA) is a lignan derived from the fruit of Schisandra chinensis, a functional food and also a traditional herbal medicine known for its hepatic protective effects. The study aims to identify potential target and regulation mechanism of SchA on NAFLD treatment. Metabolomics analysis revealed that SchA improved the abnormal metabolic profile of the liver in NAFLD mice. In addition to ameliorating lipid metabolism, SchA showed potential in elevating the levels of amino acids such as L-tryptophan, beta-alanine, L-aspartic acid, and L-tyrosine, which were deficient in NAFLD mouse livers, as well as restored the metabolism of abnormal vitamins like vitamin B6. Network pharmacology research and molecular docking suggested that GSK3β was a direct target of SchA, which was experimentally validated as well. These findings highlight the potential value of the active component SchA from Schisandra chinensis in the prevention and treatment of NAFLD.