To investigate the potential physiological functions of Benincasae exocarpium (BE) as a by-product of food processing, the chemical composition of BE alcohol extract was characterized. Mice with dextran sodium sulfate-induced colitis were treated with continuous intervention for 14 days to determine the anti-inflammatory activity of BE alcohol extract. The results showed that the contents of total phenols, total flavonoids, and total saponins in the alcohol extract were 28.34 mg gallic acid/g dry weight (DW), 47.42 catechinic acid/g DW, and 43.62 oleanolic acid/g DW, respectively. In addition, the weight loss of colitis mice was alleviated upon treatment with BE alcohol extract. The colonic length increased to 4.90 and 4.98 cm in the low- and high-dose groups, and the disease activity index decreased by 31.93% and 44.70%, respectively. Serum expression levels of TNF-α, IL-6, and mannitol were significantly decreased (P<0.05). Analysis of the gut microbiota showed that after treatment with a high dose of BE alcohol extract, the abundance of harmful bacteria such as Enterobacteriaceae, Proteobacteria, and Escherichia-Shigella decreased, whereas that of beneficial bacteria such as Bacteroidota, Muribaculaceae, and norank_f__Muribaculaceae increased. Furthermore, harmful bacteria were positively correlated with inflammatory factors and intestinal barrier damage indexes. The mechanisms underlying the reduction in systemic inflammation levels and restoration of the intestinal barrier may be associated with modulation of the gut microbiota composition. These findings provide a theoretical basis for studying the bioactivity of Benincasae exocarpium and offer valuable insights for its high-value utilization in subsequent research.