At present, inflammatory bowel disease (IBD) seriously threatens human health, and its treatment is a huge challenge for people. In our studies, we found that meisoindigo, a derivative of indirubin, significantly ameliorated dextran sulfate sodium (DSS)-induced experimental colitis in mice. Meisoindigo treatment markedly elevated the level of glutathione, while suppressed the activities of alkaline phosphatase and myeloperoxidase in colonic tissues. Moreover, the mRNA expression of vascular cell adhesion molecule 1, intercellular adhesion molecule 1, cyclooxygenase-2 which are important colitis-related molecules and the levels of the inflammatory cytokines interleukin (IL)-18, IL-1β, IL-6, tumor necrosis factor (TNF)-α and inducible nitric oxide synthase (iNOS) were suppressed dose-dependently following treatment with meisoindigo. Immunofluorescence results indicated that meisoindigo inhibited macrophage infiltration and nuclear factor (NF)-κB activation in colons from DSS-treated mice. Therefore, mouse RAW264.7 and human THP-1 cells were treated with lipopolysaccharide (LPS) alone or combined adenosine triphosphate to activate NF-κB pathway in vitro. It was shown that meisoindigo reduced the elevated levels of NO, IL-18, IL-1β and TNF-α after LPS treatment in both cells. In addition, meisoindigo showed inhibitory effects on NF-κB by using a luciferase reporter gene that depends on NF-κB. Through molecular docking, microscale thermophoresis and cellular thermal shift assay. It was further found that meisoindigo targeted transforming growth factor β activated kinase-1 (TAK1), which is an important regulator in the upstream of NF-κB pathway. In conclusion, our findings show that meisoindigo can alleviate IBD effectively at low doses, and negatively regulate proinflammatory responses by inhibiting the activation of TAK1, which provides new ideas for clinical anti-inflammatory therapy.