Obesity, a global health concern is associated with the dysbiosis of intestinal microbial composition. Previous in vitro and in vivo studies have reported the potentials of urolithins on reducing lipid accumulation. This study aims to investigate the potentials of urolithin A (Uro-A), a gut-derived metabolite of ellagitannins in reducing body weight gain through the modulation of the gut microbiota. To establish the induced obesity model in rats, animals were fed on a high-fat diet which were later administered with Uro-A. Serum biochemical parameters were quantified, and changes in the composition of the gut microbial community were analyzed using 16S rDNA gene sequencing. Our results showed that Uro-A significantly decreased the body weight gain in HFD-fed rats. Serum biochemical parameters analyses showed that this metabolite increased the level of the high-density lipoproteins while decreasing the serum levels of triglycerides, total cholesterol, and low-density lipoproteins. Furthermore, the taxonomic analysis revealed that urolithin A treatment changed the gut microbial composition. Besides, Uro-A elevated the abundance of Parabacteroides, reduced the abundances of Desulfovibrionacea, Lachnospiraceae, and Coriobacteriaceae. These modulated gut microbes are related to body weight gain, inflammation, impaired glucose, and dysfunctional lipid metabolism, which are all closely associated with obesity. Taken together, our results suggest that Uro-A possesses anti-obesity property, which may be related to the modulation of the gut microbial composition.