<p>The complex etiology of inflammatory bowel disease (IBD) presents a significant challenge to the medical field. Current IBD treatments often face issues such as patient drug resistance, high postoperative recurrence rates, and various side effects and adverse reactions associated with many therapeutic approaches. Among the existing treatments, small molecule inhibitors stand out due to their diversity, wide range of targets, and ease of administration, presenting a promising avenue to overcome challenges such as drug resistance, high recurrence rates, and systemic side effects associated with traditional biologics and immunomodulators. Small molecule inhibitors are a class of organic compounds that target multiple sites and are widely used in various diseases, such as cancer, with JAK inhibitors being a common example. Recently, there has been a growing interest in exploring the use of small molecule inhibitors to treat IBD, resulting in numerous trials and clinical studies focusing on various types of inhibitors that target different pathways. However, it is essential to consider not only the target concept but also the impact of the molecular structure on pharmacological activity. This review classifies the currently utilized small molecule inhibitors for IBD not by their targets but by their molecular chemical structures. This structural categorization provides researchers with a novel framework for investigating treatment modalities and the utilization of small molecule inhibitors in IBD, offering invaluable insights and perspectives for future research endeavors.</p>