Polysaccharides of Cistanche deserticola Ma (CDPS), with high safety and low toxicity have been reported to possess anti-inflammatory, immunomodulatory, antioxidant, anti-aging, anti-osteoporosis, antidepressant, intestinal flora regulatory and hepatoprotective properties. Nevertheless, the effects of CDPS on inflammatory bowel disease (IBD) and its underlying mechanisms have never been reported. To estimate its therapeutic potential on IBD, the extracted CDPS were characterized via utilizing a series of chemical, spectroscopic, and instrumental analyses, and the protective effects and mechanisms of CDPS in colitis mice was investigated. Our results indicated that CDPS were identified as acidic heteropolysaccharides. CDPS alleviated dextran sodium sulfate-induced IBD mice characterized by decreasing disease activity index, improving colon length and body weight, restoring histopathological lesions, inhibiting the expression of pro-inflammatory cytokine (IL-6, IL-1beta, TNF-alpha) and MPO activity, elevating the expression of anti-inflammatory cytokine (IL-10) in colon tissue. The findings manifested CDPS could mitigate the inflammation of colon. Simultaneously, CDPS inhibited the expression of genes and proteins associated with SRC/EGFR/PI3K/AKT signaling pathways, and reduced the diversity and abundance of harmful gut microbiota, including Helicobacter, Bacteroides and Colidextribacter, while descending the relative abundance of Lachnospiraceae_NK4A136_group at genus level. In summary, this work elucidated that CDPS alleviates IBD symptoms via mitigating the inflammation of colon, and modulating intestinal microbiota and SRC/EGFR/PI3K/AKT signaling pathways. It underscores the promise of CDPS as a functional food ingredient or preventive drugs for IBD.