Scope: Angelica keiskei is associated with several health benefits, but little is known about the effect of A. keiskei juice (AKJ), which is rich in polyphenols, coumarins, and other healthful agents, on high-fat diet-induced obesity or its relationship with intestinal microbiota composition changes. Methods and results: C57BL/6 mice are fed either a normal diet (ND group; n = 8), a high-fat diet (HFD group; n = 8), or a high-fat diet supplemented with AKJ (AKJ group; n = 8) for 10 weeks. The results show that AKJ prevents weight gain, lowered fat accumulation, blood glucose, serum lipid levels, hepatic steatosis, and modulates the level of expression of genes involved in lipid metabolism in mice with obesity. AKJ is found to normalize HFD-induced gut dysbiosis. Particularly, AKJ ameliorates HFD-dependent changes in the relative abundance of several taxa back to normal status (e.g., AKJ increased Bacteroides and decreased Mollicutes RF9, Ruminococcaceae UCG-014, Faecalibacterium, and Lactobacillus). Spearman's correlation analysis reveals that those genera are closely correlated with body weight, fasting serum glucose, and serum lipid levels. Conclusion: The results show that consumption of phytochemical-rich AKJ may prevent HFD-induced obesity and metabolic disorders via changes in metabolic genes and gut microbiota composition.