Anthocyanin-rich extracts have shown anti-inflammation activity in mouse colitis models. Cyanidin-3-glucoside (C3G) is one of the widespread anthocyanins in plants, and cyanidin (Cy) is the aglycone of C3G that can be generated in intestine under gut microorganism metabolism. To explore the anti-inflammatory activity of single anthocyanins compound and show the potential mechanism, the protective effects of C3G and its aglycone Cy on 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced colitis in mice and lipopolysaccharide (LPS)-stimulated Caco-2 cellular monolayer inflammation were studied. The results showed that both C3G and Cy significantly improved the clinical symptoms and relieved the histological damage in TNBS-challenged mice. The activity of myeloperoxidase and the excretion of inflammatory cytokines tumor necrosis factor-, interleukin-1, interleukin-6, and interferon- were also significantly inhibited at the administration dosage of 200 mol/kg. studies showed that when LPS-stimulated Caco-2 cells were pretreated with C3G and Cy, the destruction of the intestinal epithelial barrier was ameliorated due to the improvement of the transepithelial electrical resistance and Lucifer yellow flux values, while there were no significant difference between C3G and Cy groups at the same dosage. Similarly, both C3G and Cy suppressed nitric oxide production and inflammatory cytokines secretion of LPS-induced Caco-2 cells. C3G and its aglycone Cy had similar anti-inflammatory activity in both colitis mice and Caco-2 cells. The results suggest that C3G and Cy may exert anti-inflammatory effects by protecting the intestinal barrier as well as by suppressing inflammatory cytokine secretion. Thus, C3G or Cy could be potential preventive agents or supplementary medicines for inflammatory bowel disease.