α-Amylase inhibitors (α-AI) have great potential to treat obesity. In this study, an α-AI enriched extract (α-AIE) with a specific activity of 1027.1 ± 154.2 (U per mg protein) was prepared from white common bean (Phaseolus vulgaris L.) seeds. Its anti-obesity effect and gut microbiota modulation properties were verified in high-fat diet-induced obese rats. The intake of the α-AIE significantly reduced body weight gain and improved serum lipid levels (p < 0.05). In addition, rats fed the α-AIE diet exhibited higher total short-chain fatty-acid (SCFA) concentrations (p < 0.05) in their colonic contents. β-Diversity analysis, principal component analysis and a Venn diagram showed that α-AIE administration changed the gut microbiota composition. At the phylum level, the relative abundances of Firmicutes and Proteobacteria decreased and the relative abundances of Bacteroidetes and Akkermansia increased. In addition, 89 operational taxonomic units (OTUs) significantly responding to the high-fat diet and 30 OTUs significantly responding to the α-AIE were identified. The OTUs enriched by the α-AIE were mainly assigned to putative SCFA-producing bacteria, including Bacteroides, Butyricoccus, Blautia and Eubacterium. Twenty-two OTUs were found to be significantly correlated with obesity indexes. Taken together, the present results suggest that the intake of the α-AIE attenuated obesity and modulated gut microbiota.