A high-fat diet (HFD) has been a major contributor to increasing morbidity caused by metabolic syndromes. Functional foods from natural sources are potential choices for addressing metabolic diseases because they provide many health benefits with a low level of adverse side effects. In our former reports, fucoidan from Pearsonothuria graeffei (fuc-Pg), a type of sulfated polysaccharides with a repeating structure, was shown to be a potential functional food ingredient. In this work, we investigated the effects of fuc-Pg on gut microbiota dysbiosis and metabolic syndromes caused by HFD. Our results indicated that fuc-Pg could reduce weight gains, alleviate hyperlipidemia, and protect the liver from steatosis in HFD-fed mice. Meanwhile, fuc-Pg decreases serum inflammatory cytokines and reduces macrophages infiltrating into adipose tissue. The gut microbiota dysbiosis caused by HFD was alleviated by administration of fuc-Pg, mainly working in the colon. Fuc-Pg increased abundances of Bacteroidetes and Actinobacteria while decreased Firmicutes and Proteobacteria. Our results indicated that fuc-Pg could be a functional food for gut microbiota dysbiosis and metabolic syndromes.