Recently, fucoidan has been proposed as a potential prebiotic agent for functional food and pharmaceutical development. However, while previous studies illustrated favorable modulations of gut microbiota by fucoidan, changes in the overall microbial structure remain elusive. In the present study, modulations of gut microbiota by different fucoidans were studied using high throughput sequencing and bioinformatics analysis. We found that at the expense of opportunistic pathogenic bacteria such as Peptococcus, the abundance of beneficial bacteria including Lactobacillus and Ruminococcaceae was significantly increased in response to fucoidan treatment. Besides, by maintaining a more balanced composition of gut microbiota, dietary fucoidan also significantly reduced the antigen load and the inflammatory response in the host as evidenced by the decreased serum lipopolysaccharide-binding protein levels. Collectively, our results indicate that fucoidan can be used as a gut microbiota modulator for health promotion and treatment of intestinal dysbiosis.