This study enrolled 94 patients with UC or CD. Two groups received either 8-week intestinal bacterial transplant capsule therapy or biological therapy, respectively. The control group received biological therapy alone, while the experimental group received biological therapy combined with FMT. Both groups were followed up for 52 weeks after discharge. The efficacy of FMT capsule therapy on the subjects' UC or CD symptom-related scores and its effect on remodeling the intestinal flora were observed, and its safety was verified.