In a previous study, we fractionated rhamnogalacturonan (RG)-I rich polysaccharides with intestinal immunomodulatory effect from crabapple. MP-PE-I, which is rich in RG-I, was determined to be branched into arabino-β-3,6 galactan, arabinan, and galactan in the RG-I main chain region where rhamnose and galacturonic acid are alternately bound, by component sugar, β-glucosyl yariv reactivity, and partially methylated alditol acetate analysis. Oral administration of MP-PE-I significantly improved blood around the anus, body weight change, and disease activity index (DAI) score on the DSS-induced inflammatory bowel disease (IBD) model. Three major organs, the heart, kidney, and liver, were harvested from the animals and weighed to evaluate the toxic effect of MP-PE-I, oral administration of MP-PE-I for 3 weeks was well tolerated and safe. MP-PE-I oral administration alleviated colon length shortening and spleen enlargement compared with the DSS-induced group. MP-PE-I not only decreased levels of pro-inflammatory factors but also increased levels of anti-inflammatory factors. In addition, contents of short chain fatty acids (SCFAs) such as acetic acid, propionic acid, and butyric acid increased in the fecal and cecum compared to the DSS-induced group. Consequently, the aforementioned results suggested that RG-I rich polysaccharide isolated from crabapple could be an effective material for IBD treatment.