Background: Hepatic lipid metabolism disorder has been linked to a wide range of diseases. Aspalathin is a flavonoid enriched in rooibos tea and has shown capacity to protect against hyperlipidemia, oxidative stress and inflammation. In the current study, we investigated the functional role of aspalathin in regulating liver metabolism and gut microbiota in the context of a high-fat diet (HFD). Methods: Male mice were fed a control diet or HFD, then HFD-fed animals were treated with or without aspalathin-rich extract (ASE). Hepatic neutral lipids were detected using oil red O staining and a colorimetric assay. Expression of cholesterol metabolism-, lipogenesis- and fatty acid β-oxidation-associated genes was measured. Gut microbiota was analyzed using 16S rRNA sequencing and bioinformatic approaches. Results: HFD-fed mice had markedly higher levels of triglycerides and cholesteryl esters and downregulated expression of cholesterol metabolism-, transport- and lipogenesis-related genes in the liver. ASE administration counteracted HFD-induced effects. In addition, HFD altered the composition, diversity and metabolic pathways of the gut microbiota. The richness of beneficial bacteria, particularly the butyrate-producing bacteria, was significantly decreased. The altered metabolic pathways are involved in the metabolism of carbohydrates, lipids, amino acids and nucleotides, as well as mitochondrial function. ASE treatment reversed most of the alterations back to the characteristics of the control group. Conclusions: Our results demonstrated the potential of ASE improving liver lipid metabolism and gut microbiota in the scenario of a high-fat diet, providing insights into future studies on the mechanism of ASE regulating lipid metabolism disorder.