Human clostridia play a very important role in the human gastrointestinal tract. In this study, an irritable bowel syndrome (IBS) model was established using the water avoidance stress (WAS) method, Mice subjected to WAS were treated with saline, human clostridial solution (enriched with human clostridial cluster IV), prucalopride, the TPH antagonist PCPA or the 5-HT4 antagonist RS39604 for 1 week. TPH1, 5-HT4, PKA, CREB, and pCREB expression decreased in the distal colon and hippocampus of WAS mice, colonic SLC6A4 expression decreased and hippocampal SLC6A4 expression increased, and the number of 5-HT4-positive cells decreased. Human clostridia treatment was superior to the remaining treatments after 1 week; Clostridia-treated mice showed increased colonic and hippocampal expression of TPH1 and 5-HT4 signaling pathway-related proteins, increased colonic expression of SLC6A4, decreased hippocampal SLC6A4 expression, and increased numbers of 5-HT4-positive colonic cells. The use of PCPA or RS39604 influenced the effect of bacterial solution treatment, and human clostridia elevated fecal isovaleric acid levels. In conclusion, human clostridia improved visceral hypersensitivity by upregulating 5-HT4 signaling protein expression in the distal colon and hippocampus, demonstrating its therapeutic potential.