Polyacylated anthocyanins are known for their enhanced stability and immunosuppressive properties. Although peonidin-3-O-(3,6-O-dimalonyl-β-D-glucoside) (P3GdM) from black corncobs has demonstrated notable antibacterial and stress-resistance effects in plants, its regulatory role in inflammatory bowel disease (IBD) remains unexplored. In this study, P3GdM was isolated from black corncobs, and its potential as a treatment for dextran sulfate sodium (DSS)-induced colitis in mice was evaluated. The findings revealed that P3GdM significantly mitigated clinical symptoms, reduced the disease activity index (DAI), suppressed the production of pro-inflammatory cytokines and endotoxins, and repaired the intestinal barrier. Furthermore, P3GdM markedly improved DSS-induced gut microbiota dysbiosis, significantly increasing microbial diversity and enhancing the relative abundance of critical bacterial species such as Akkermansia muciniphila and Lactobacillus reuteri, while also stimulating the production of short-chain fatty acids (SCFAs) and lactic acid. Correlation analyses further revealed strong associations between key microbial taxa, pro-inflammatory factors, clinical symptoms, tight junction proteins, and SCFAs. These findings provide support for the potential of P3GdM as an adjunct therapy for intestinal disorders, particularly colitis.