Panax ginseng is a traditional medicinal plant used in most Asian countries to cure many diseases. The benefits of ginseng are due to its primary active component, polysaccharides. Gut microbiota dysbiosis is a worldwide problem associating with antibiotic use. The objective of this study was to investigate the effects of ginseng polysaccharides (WGP) on the diversity of the gut microbiota in mice with antibiotic-associated diarrhea. Compared to diarrhea mice, WGP significantly changed the composition and diversity of the gut microbiota. Specifically, WGP increased the relative abundance of the phylum Firmicutes and decreased the relative abundance of the phyla Bacteroidetes, Proteobacteria and Actinobacteria. At the genus level, WGP increased the relative abundance of Lactobacillus, Lactococcus, and Streptococcus, but decreased the relative abundance of Bacteroides. The key phylotype of beneficial bacteria in the gut microbiota that responded to WGP was Lactobacillus. In addition, WGP also reversed carbohydrate, amino acid and energy metabolism to normal levels, thereby promoting the recovery of the mucosal structure. Taken collectively, our results indicate that WGP altered the composition and diversity of the gut microbiota in mice with antibiotic-associated diarrhea, restored the gut microbiota, balanced metabolic processes, and promoted the recovery of the mucosa.