The current study employed high-fat diet (HFD) induced murine model to assess the relationship between the lipid-lowering effect of aged citrus peel (chenpi) extract and the alterations of gut microbiota. The results showed that intake of chenpi extract for 12 week dose-dependently suppressed HFD-induced body weight, food intake, Lee's index, together with decreased the level of fasting blood glucose, total cholesterol, triglyceride, and low-density lipoprotein cholesterol. Moreover, chenpi extract administration up-regulated the abundance and diversity of fecal microbiota and down-regulated the ratio of Firmicutes-to-Bacteroidetes, which was characterized by the lower family of Lachnospiraceae, Helicobacteraceae, and Desulfovibrionaceae, and higher family of Bacteroidales_S24-7, Bacteroidaceae, Rikenellaceae, and Ruminococcaceae. Consistently, at the genus levels, chenpi extract treatment reversed the expansions of Helicobacter, Lachnospiraceae_UCG-006, and Desulfovibrio, while increased the abundance of Bacteroides, Rikenellaceae_RC9_gut_group, and Alistipes (belonging to Rikenellaceae family), Anaerotruncus and Odoribacter (belonging to Ruminococcaceae family), which were significantly negatively correlated with the levels of the serum lipid parameters. In conclusion, our findings indicated that anti-obesity ability of chenpi extract might be related to the improvement of gut microbiota imbalance. PRACTICAL APPLICATIONS: With the improvement of living standards, the incidence of metabolic diseases such as obesity, hypertension, and diabetes has increased significantly, and it has become a public health problem that seriously affects the health of the people. Chenpi contains a large amount of active ingredients, flavonoids, and other compounds, which can promote the absorption of the digestive system and have good effects on diseases such as the cardiovascular system. Our previous study has confirmed that the chenpi extract effectively regulated the glucose and lipid metabolism disorder induced by high-fat diet. However, it is not clear whether the effect is closely related to the improvement of gut microbiota. Accordingly, our result would provide a theoretical basis for future research on the relationship between obesity, chenpi extract, and gut microbiota, and support additional understanding of its potential anti-obesity effects.