A ulcerative colitis (UC) model was established using dextran sulfate sodium (DSS), and intervention with Malonyl Ginsenosides( MGR) was employed. Biochemical markers in serum and colonic tissues of UC mice were measured, along with the expression of the PI3K/AKT/NF-κB signaling pathway in UC mice, and the alteration in intestinal microbiota was analyzed. Results revealed that MGR significantly decreased levels of IL-6, IL-1β, and TNF-α in serum, inhibited the elevation of MDA and MPO levels, and restored SOD levels in colonic tissues. Additionally, MGR downregulated the expression of p-PI3K, p-AKT, TLR4, and NF-κB. Furthermore, MGR modulated the composition and diversity of intestinal microbiota, reduced the relative abundance of harmful bacteria such as Desulfovibrionaceae, Parasutterella, and Helicobacter, while increased that of beneficial bacteria like Prevotellaccae and Lactobacillus. In conclusion, MGR may exert its anti-UC effects by suppressing inflammation, oxidative stress, and rebalancing intestinal microbiota.