Acute bacterial diarrhea is a severe global problem with a particularly high incidence rate in children. The microecology inhabiting the intestinal mucosa is the key factor leading to diarrhea. Gegen Qinlian decoction (GQD) is used to treat bacterial diarrhea, however, its underlying mechanism remains unclear. Thus, this study aimed to clarify the restorative effect of GQD on the intestinal barrier from the perspective of gut microbiota. A Tibetan piglet model with bacterial diarrhea was established through orally administered Escherichia coli, and diarrheal piglets were treated with GQD for three days. After treatment, GQD significantly ameliorated the diarrheal symptoms. GQD decreased the levels of IL-6, LPS, and DAO, and increased SIgA, ZO-1, and occludin levels in intestinal mucosa, indicating the restoration of intestinal barrier. GQD modulated the microbial compositions inhabited on the intestinal mucosa, especially an increase of the Lactobacillus. Spearman analysis showed that Lactobacillus was the key genus of intestinal barrier-related bacteria. Bacterial culture in vitro validated that GQD directly promoted Lactobacillus growth and inhibited E. coli proliferation. Moreover, the expressions of TLR2, MyD88, and NF-κB in the colon decreased after GQD treatment. In conclusion, GQD may treat diarrhea and restore the intestinal mucosal barrier by facilitating Lactobacillus growth and inhibiting the TLR2/MyD88/NF-κB signaling pathway.