Ulcerative colitis (UC) is a temporary incurable inflammatory bowel disease. Alpinia oxyphylla fructus polysaccharides (AOFPs) have anti-inflammatory, antioxidant, and other biological activities. In order to explore the therapeutic effect of AOFPs on UC, this study used deionized water, NaCl, HCl, and NaOH to extract AOFPs, and their protective effects on UC were evaluated by dextran sulfate sodium-induced UC mouse model. The results showed that extraction solvents had significant effects on the yield, molecular weights, monosaccharide compositions, total sugar contents, uronic acid contents, protein contents, and surface morphology of AOFPs. Histopathological analysis found that AOFPs could significantly reduce inflammatory cell infiltration and improve crypt morphology. ELISA and real-time PCR results show that AOFPs can downregulate the contents of TNF-α, IL-1β, and IL-6 and upregulate the content of IL-10. Western blot results show that AOFPs could enhance the expression of E-cadherin, occludin, claudin 1, and ZO-1. In addition, AOFPs improved the richness and diversity of intestinal flora and reshaped the intestinal flora by increasing the proportion of beneficial bacteria and inhibiting the proportion of harmful bacteria. These results indicate that AOFPs have therapeutic effects on UC. This may be due to the regulatory effect of AOFPs on the intestinal flora, restoring intestinal inflammation and permeability.