Inflammatory bowel disease (IBD) refers to a long-term and nonspecific disorder that affects the intestines. Despite the availability of various therapeutic means, including anti-inflammatory drugs, immunosuppressants, and biologics, their therapeutic efficacy remains suboptimal, accompanied by significant adverse effects. Natural products have garnered attention as a promising area of research due to their distinctive pharmacological activities and favorable safety profiles. However, the applications of some natural products are constrained by inherent limitations, such as poor solubility and bioavailability. To address the shortcomings of natural products-drugs, novel drug delivery systems (DDSs) such as micro/nano, hydrogel, and probiotics have been developed to facilitate the delivery of natural products for the treatment of IBD. Additionally, novel natural products can be directly engineered into DDSs to target IBD lesion sites. Natural products-integrated DDSs can enhance therapeutic specificity, extend the duration of therapeutic action, and minimize side effects. This review elucidates those natural products and their associated DDSs, such as micro/nano systems, hydrogels, and probiotics, provide efficacious treatment for IBD by means of reducing oxidative stress, repairing the intestinal barrier, modulating intestinal microbiota, and alleviating intestinal inflammation.