Anthocyanins are phytonutrients with physiological activity belonging to the flavonoid family whose transport and absorption in the human body follow specific pathways. In the upper gastrointestinal tract, anthocyanins are rarely absorbed intact by active transporters, with most reaching the colon, where bacteria convert them into metabolites. There is mounting evidence that anthocyanins can be used for prevention and treatment of intestinal diseases, including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), and colorectal cancer (CRC), through the protective function on the intestinal epithelial barrier, immunomodulation, antioxidants, and gut microbiota metabolism. Dietary anthocyanins are summarized in this comprehensive review with respect to their classification and structure as well as their absorption and transport mechanisms within the gastrointestinal tract. Additionally, the review delves into the role and mechanism of anthocyanins in treating common intestinal diseases. These insights will deepen our understanding of the potential benefits of natural anthocyanins for intestinal disorders.