Gut microbiota dysbiosis is associated with inflammation and many chronic diseases. The present study investigated the efficacy of mung bean seed coat extract (MSE) on gut microbiome modulation and the attenuation of inflammatory markers in high-fat diet (HFD)-fed rats. The high-throughput sequencing of the 16S rRNA showed the low dose (0.3%) of MSE improved HFD-induced gut microbiota dysbiosis and enhanced the gut microbiota richness. The low dose of MSE showed a significant increase in the abundance of beneficial bacteria, particularly Blautia and Lactobacillus, and decreased abundance of potentially pathogenic bacteria (Escherichia-Shigella). The low dose of MSE also significantly decreased IL-1β mRNA expression and tended to lower IL-6, TNF-α, and LPS levels. In conclusion, this study suggested that the MSE could modulate gut microbiota and reduce inflammatory responses in HFD-fed rats and this indicated the potential health properties of mung bean seed coat. This research provides informative support for the application of mung bean seed coat as functional ingredients.