Abstract：Objective: To investigate the changes of intestinal flora as well as function after treatment of rats with antibiotic-associated diarrhea with GeGen QinLian Decoction. Methods: Sixty SPF-grade male and female SD rats were fed for 7 days and randomly divided into blank and modeling groups according to 1:5. Rats in the modeling group were modeled by gavage with clindamycin 250 mg/kg once a day for 7 consecutive days. After successful modeling, the rats were randomly divided into the model group (Mod), the high dose group of GeGen QinLian Decoction (GQD-H), the medium dose group of GeGen QinLian Decoction (GQD-M), the low dose group of GeGen QinLian Decoction (GQD-L), and the Live Bifidobacterium Power group (LBP), with 10 rats in each group. According to the administered doses of GQD-H (10.08 g/kg), GQD-M (5.04 g/kg), GQD-L (2.52 g/kg), and LBP (0.15 g/kg) by gavage, the blank and model groups were given an equal volume of saline by gavage once a day, and feces were collected after 7 consecutive days of administration for macro-genomics sequencing analysis. Results: α-diversity and β-diversity suggested that there was a difference in intestinal microbial diversity between the Mod group and the GQD-treated group; GQD increased the abundance of the phylum Thick-walled Bacteria and decreased the abundance of the phylum Aspergillus at the phylum level. Increased relative abundance of intestinal mucus fungi Blautia, Bacteroides, Thomasclavelia, Mediterraneibacter and decreased relative abundance of Adlercreutzia, Muribaculum, Escherichia at the genus level; GQD up-regulated amino acid metabolic pathway, carbohydrate metabolic pathway, and immune disease pathway. Conclusions: GQD intervention in AAD improves the abundance ratio of beneficial and pathogenic intestinal bacteria, which in turn reduces the intestinal inflammatory response and repairs the intestinal immune system.