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Indigo naturalis (IN) prepared using a novel method (NIN) has exhibited beneficial efficacy against inflammatory and cancerous colonic cells. However, the underlying mechanism still remains to be elucidated. This study aimed to construct an inflammation model by the HT\u201029 colonic cancer cell line and to investigate the effect of NIN on an inflammatory cancer state and the possible mechanism. The results showed that NIN could reduce the increased expression of pro\u2010inflammatory cytokine IL\u20101\u03b2 in the inflammatory cancer cells and attenuate the inflammatory response; elevate the low expression of MUC2 in the inflammatory cancer state and restore the mucin secretion function; and inhibit the proliferation of HT\u201029 cells. Based on the activation of the aryl hydrocarbon receptor (AhR) signaling pathway, NIN increases the expression of the Wnt\/\u03b2\u2010catenin signaling pathway inhibitor Rnf43, inhibits the expression of nonphosphorylated \u03b2\u2010catenin, and reduces the level of the pathway downstream target gene Axin2, which in turn inhibits the Wnt\/\u03b2\u2010catenin signaling pathway and inhibits the expression of Lgr5, a stem cell gene of colorectal cancer (CAC). The production of the above effects of NIN was blocked by the AhR antagonist CH223191. The in vitro studies verified that NIN alleviated UC by activing AhR signaling pathway, which in turn inhibited the Wnt\/\u03b2\u2010catenin signaling pathway. The possible mechanism of NIN on UC could be explained starting from the inflammation\u2010cancer transformation. 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