The incidence rate of colon cancer ranks the third among malignant tumors worldwide. Gloeostereum incarnatum (GI), a fungus with homology of medicine and food, has multiple pharmacological activities. It was investigated in this study that the anti-colon cancer effect of polysaccharides purified from GI (GIPS) in ApcMinC/Gpt mice (an in situ colon cancer mouse model). Eight-week administration with GIPS at doses of 30 or 90 mg/kg strongly inhibited tumor growth including the reduction on numbers and the suppression of the size without influencing the animals’ body weight and organ functions. According to the proteomics performing by antibody array, among 308 detected cytokines, GIPS significantly regulated 89 of them. Compared with vehicle-treated mice, GIPS effectively reduced the levels of interleukin (IL)-1β, IL-4, IL-6, IL-17, IL-22, tumor necrosis factor (TNF)-α, matrix metalloproteinase (MMP)-2, and enhanced the levels of IL-15 and IL-18 in serum and/or colon tissues, which suggested its anti-inflammation of GIPS. GIPS suppressed nuclear aggregation of β-catenin, affected the expression of WNT1 and related proteins, thereby regulated the activation of the Wnt signaling. Altogether, GIPS can inhibit the growth of colon cancer, at least partially, via inhibiting the Wnt/β-catenin signaling pathway.