Inflammatory bowel disease (IBD) is characterized by recurrent attacks and long courses, and the number of patients has expanded rapidly year by year. Additionally, current conventional strategies exist serious adverse effects. In this case, it is an urgent issue to find out an effective and safe treatment. Functional oligosaccharides possess safe and excellent physiological activities, and have attracted enormous attention due to their great therapeutic potential for IBD. This review emphasizes the attenuating effects of distinct functional oligosaccharides on IBD and their structure, and summarizes the main mechanisms from the aspects of regulating intestinal flora structure, repairing intestinal barrier, modulating immune function and mediating related signaling pathways in order to reveal the relationship between functional oligosaccharides, immune regulation, intestinal epithelial cells, gut flora and IBD treatment. Oligosaccharides possess excellent protective effects on IBD, and can be considered as safe and functional ingredients in the health food and pharmaceutical industry.