Objective To explore the effects of gardenia extract on intestinal mucosal microbiota and body weight in mice fed a high-fat diet, and to explore the microecological mechanism of gardenia extract in obese mice.Methods The potential mechanism of gardenia extract in treating obesity is predicted by network pharmacology and molecular docking technology. Additionally, 24 SPF C57BL/6 male mice are randomly assigned into a blank group (8 mice) and a model group (16 mice). The model group receives a high-fat diet for 12 weeks, while the blank group receives an ordinary diet. After modeling, 12 successfully modeled mice are randomly divided into a natural recovery group (M group, n=6) and a gardenia extract group (Ga group, n=6). The 6 mice in the blank group are classified as the normal group (C group, n=6). The Ga group is administered with gardenia extract at a dose of 220 mg/(kg·d) for 4 weeks, while the other two groups are gavaged with an equal volume of sterile water. After the intervention, small intestinal mucosa samples of mice in each group are obtained for characteristic analysis of the intestinal mucosal microbiota by the 16S rRNA gene high-throughput sequencing.Results The network pharmacological analysis shows that gardenia extract can regulate 113 targets related to obesity, and the main regulatory pathways are metabolism and inflammatory reaction. The molecular docking results indicate that quercetin and other key components of gardenia extract exhibit high binding energy with core targets, such as TP53 and TNF. The in vivo experimental results reveal that after intervention, the weight gain rate of mice in the Ga group is slower than that in the M group. The α diversity of the intestinal mucosal microbiota exhibits an upward trend, with significant changes in the β diversity (P<0.05). On the phylum level, a significant increase occurs in the abundances of Actinobacteria and Verrucomicrobia (P<0.05), as well as Cyanobacteria. At the genus level, a significant increase occurs in the abundance of Vibrio (P<0.05). Lachnospiraceae NK4A136 group and Veillonella are the characteristic bacteria in the M group.Conclusion In treating obesity, gardenia extract has the characteristics of multi-target and multi-channel, with the core targets including lipid metabolism and inflammatory reaction. Gardenia extract, which changes the intestinal microbiota community, may slow down the weight growth trend of obese mice by up-regulating Actinobacteria, Verrucomicrobia, and Vibrio, while down-regulating Veillonella.