The incidence and prevalence of inflammatory bowel diseases (IBD), mainly comprising ulcerative colitis and Crohns disease, are increasing dramatically worldwide.Immunomodulators and biological agents can help but cause severe side effects in long-term use.As such, complementary and alternative medicine, in particular herbal remedy, is becoming more and more popular in the treatment of IBD patients.Many natural compounds alone or as a combination have been used in clinical trials and some have been proven promising in IBD treatment.To achieve a better understanding of herbal therapy, researchers are focusing on understanding the underlying mechanisms by using experimental rodent models.The mechanism of the pathogenesis of IBD is complex involving both environmental and genetic factors.IBD is considered as a consequence of impaired epithelial barrier function, gut microbiota dysbiosis, and aberrant immune response.Studies have demonstrated that herbal medicine can improve epithelial proliferation and barrier integrity, restore microbiota homeostasis, and suppress hyper-immune reaction.This review is to summarize current understanding of the molecular basis of herbal treatment of IBD at the levels of epithelial, microbial, and immune regulation.