Recently, fucoidan has been proposed for use as a potential anti-inflammatory drug. The purpose of this study was to investigate the mechanism of fucoidan in the treatment of ulcerative colitis. We compared the anti-inflammatory effects of fucoidan and fucose induced by dextran sulfate sodium, and the effects of fucoidan and fucose on the gut microbiota of mice. Our results showed that low-dose fucoidan significantly improved weight loss, disease activity index scores, colonic shortening, colonic histopathological damage, intestinal fatty acid binding protein 2 levels, and the expression of Occludin, Claudin-4, and Claudin-1. However, both high-dose fucoidan and fucose did not perform as well as low-dose fucoidan as described above. In addition, 16S rDNA high-throughput sequencing showed that low-dose fucoidan significantly increased the abundance of Alloprevotella, and fucose significantly increased Ruminococcaceae, but neither significantly reversed the imbalance in the gut microbiota. Therefore, we inferred that the regulation of fucoidan on colitis has a unique and complex mechanism, and it is not completely dependent on degradation to fucose to relieve ulcerative colitis, nor is it achieved only by regulating the gut microbiota. The mechanism by which fucoidan treats colitis may also include reducing inflammatory cell infiltration and increasing intestinal barrier function.