The aim of this study was to explore the protective mechanism of WLY-0, a polysaccharide extracted from Huangshui, on the intestinal barrier by RNA sequencing (RNA-seq) using the Caco-2 cell model. The results showed that the differential genes between the WLY-0 treatment group and the lipopolysaccharide (LPS)-induced injury group were enriched in the mitogen-activated protein kinase (MAPK) signaling pathway. Subsequently, Western blot was used to verify the effect of WLY-0 on the expression of key proteins in the MAPK signaling pathway. It was found that the addition of WLY-0 significantly inhibited the phosphorylation of p38 and c-Jun N-terminal kinase (JNK) and promoted the phosphorylation of extracellular signalregulated kinase (ERK) (P < 0.05). Meanwhile, the mRNA expression of the downstream pro-inflammatory factors IL-6, TNF-α, and IL-8 decreased by 53.34%, 44.56%, and 37.16%, respectively, while those of the anti-inflammatory factors IL-10 and IL-37 increased by 6.96 and 19.54 times, respectively. These results indicated that WLY-0 protects against LPS-induced intestinal barrier injury by altering the expression of inflammation-related genes through the regulation of the MAPK-mediated anti-inflammatory signaling pathway. This conclusion provides a theoretical basis for developing adjuvant therapeutic products based on Huangshui polysaccharides for inflammatory bowel disease.