Abstract: The dried roots of Berberis heteropoda Schrenk have traditionally been used to treat acute gastroenteritis and dysentery. The aim of this study was to confirm the antibacterial activity of an extract of Berberis heteropoda Schrenk root in vitro and its therapeutic effects on rats with diarrhea-predominant irritable bowel syndrome (D-IBS) in vivo, as well as to identify the related signaling pathways. A water extract of Berberis heteropoda Schrenk root (BHS) inhibited the growth of S. aureus, E. coli, P. aeruginosa and S. faecalis. BHS potentially damaged the structure of the bacterial cell membrane and decreased the activity of some membranous enzymes, eventually killing the S. aureus, E. coli, P. aeruginosa and S. faecalis bacteria. Oral administration of BHS (low, middle and high dose group, L, M and H) significantly alleviated the abdominal pain, diarrhea, and depression-like symptoms of D-IBS rats, and the efficacy index ranged from 30% to 60%, indicating that the BHS treatment was effective. BHS (L, M and H) alleviated the abnormal pathological changes in the brain, as evidenced by HE staining. The expression of CHAT, 5-HT, C-FOS and CGRP was reduced by the BHS treatment (L, M and H). Our findings provide novel insights into the use of the natural product BHS to inhibit pathogenic bacteria by destroying the bacterial structure, indicating that BHS possesses certain biological activities. Furthermore, BHS has the potential to alleviate diarrhea, abdominal pain and depression-like behaviors in D-IBS rats by regulating the brain-gut peptide levels.