Excessive generation of reactive oxygen species (ROS) resulting in oxidative stress and plays a crucial role in the progression of inflammatory bowel disease (IBD), which may in turn serve as a potential therapeutic target. To date, efforts on ROS scavenging systems have been focused predominantly on metal oxide nanoenzymes and polyphenol-based nanomaterials. Polyphenols, as a natural plant extract, have attracted increasing interests and showed great antioxidant properties in IBD therapy. The unique catechol groups in polyphenols allowing them to interact with biomolecules, such as proteins and nucleic acids. Additionally, the strong metal ion chelating ability of catechol enriched the structure and function of nanomaterials. This characteristic not only improves the physicochemical properties of polyphenols based nano-carriers but also enables innovative designs of multifunctional drug delivery systems (DDSs). To date, research on polyphenol-based DDSs has increased, including epigallocatechin gallate (EGCG), curcumin (CUR), resveratrol, tannic acid (TA), rosmarinic acid (RA) and dopamine (DA). In this review, we mainly focus on the design and application of natural polyphenol based nanomaterials in IBD, providing a comprehensive discussion on the use of polyphenols in DDSs. We will also discuss the potential challenges in innovative drug delivery strategies, including their impact on the physical and chemical properties of drug delivery systems.