Inflammatory bowel disease (IBD) mainly consists of Crohn’s disease (CD) and ulcerative colitis (UC). Rapid progress has been made to understand the interaction between the gut microbiota and IBD, which provides the rationale for administering probiotic agents in the medical treatments of IBD. It is now widely accepted that probiotic therapy is a helpful option for UC and pouchitis, but stays controversial for CD. Probiotics help to alter the gut dysbiosis, improve the function of mucosal barrier, stimulate the development of innate and adaptive immunity and modulate bacterial metabolites. Although probiotics have shown promise in the treatment of IBD, further controlled studies, enrolling larger numbers of patients, are needed to identify the therapeutic role of probiotics.