Flos Abelmoschus manihot is widely used as traditional drug in China. Abelmoschus manihot (AM) extracted from Flos Abelmoschus manihot that has been applied for treating chronic inflammatory diseases. Here we showed that AM significantly alleviated DSS-induced colitis in mice. AM modified gut microbiota composition, increased microbial diversity, and in particularly, elevated the abundance of short chain fatty acids (SCFAs)-producing gut microbiota in colitic mice. Consequently, levels of SCFAs especially butyrate and acetate were increased upon AM treatment, which, primarily through peroxisome proliferator-activated receptor gamma (PPARγ) pathway, led to the enhanced Treg generation and the suppressed Th17 development. Together, we herein provide the first evidences to support that AM, a natural plant-derived complex, can potentially reset gut microbiome and metabolism, resume immune and tissue homeostasis, and hence prevent colitis, which may provide a new perspective on IBD pathogenesis and suggest a novel microbiota-targeting therapy for inflammatory gut diseases.