Alginate oligosaccharides are associated with some beneficial health effects. Gut microbiota is one of the most recently identified factors in the development of several metabolic diseases induced by high-fat diet. Our objective was to evaluate how alginate oligosaccharides impact on high-fat diet-induced features of metabolic disorders and whether this impact is related to modulations in the modulation of the gut microbiota. C57BL/6J mice were fed with chow diet, high-fat diet, or high-fat diet supplemented with alginate oligosaccharides for 10 weeks. Alginate oligosaccharide treatment improved lipid metabolism, such as reducing levels of TG and LDL-C and inhibiting expression of lipogenesis genes. Alginate oligosaccharide administration reduced the levels of fasting blood glucose and increased the levels of serum insulin. Alginate oligosaccharide treatment was found to lower the expression of markers of inflammation, including IL1 beta and CD11c. Alginate oligosaccharide treatment modulated gut microbial communities and markedly prompted the growth of Akkermansia muciniphila, Lactobacillus reuteri, and Lactobacillus gasseri. Additionally, alginate oligosaccharide intervention significantly increased concentrations of short-chain fatty acids, such as acetic acid, propionic acid, and butyric acid, as well as decreased levels of endotoxin. Alginate oligosaccharides exert beneficial effects via alleviating metabolic metrics induced by high-fat diet, which is associated with increase in A. muciniphila, L. reuteri, and L. gasseri, as well as the release of microbiota-dependent short-chain fatty acids and inhibition of endotoxin levels.