The gastrointestinal tract, the second largest organ in the body, plays an important role in nutrient and mineral intake through the intestinal barrier. Dysfunction of intestinal permeability and related disorders commonly occur in patients with inflammatory bowel disease (IBD), one of the health problems in the Western societies that are considered to be mainly due to the Western diet. Although the exact etiology of IBD has not been elucidated, environmental and genetic factors may be involved in its pathogenesis. Many synthetic or biological drugs, such as 5-aminosalicylic acid corticosteroids as anti-inflammatory drugs, have been used clinically to treat IBD. However, their long-term use exhibits some adverse health consequences. Therefore, many researchers have devised alternative therapies to overcome this problem. Many studies have revealed that some functional nutrients in nature can relieve gastrointestinal inflammation by controlling proinflammatory cytokines. In this study, we review the ability of functional nutraceuticals such as phytochemicals, fatty acids, and bioactive peptides in improving IBD by regulating its underlying pathogenic mechanisms.