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Dietary fiber is regarded to improve host metabolic disorders through modulating gut microbiota. The study was to investigate the effects of inulin with different degree of polymerization (DP) on adiposity, related metabolic syndrome, and the possible mechanisms from the points of gut microbiota and metabolite changes. C57Bl/6J male mice were randomly allocated to normal diet (ND) group, high‐fat diet (HFD) group, two HFD groups with short‐chain inulin (HFD‐S) and medium and long‐chain inulin (HFD‐ML) for 8 weeks. Compared with HFD treatment, ML‐inulin supplementation significantly decreased weight gain, hepatic steatosis, chronic inflammation, and increased insulin sensitivity, energy expenditure and thermogenesis. This could be mimicked by S‐inulin supplementation to some degree although it is not as effective as ML inulin. Also, mice treated with S and ML inulin had a remarkable alternation in the composition of gut microbiota and increased the production of short‐chain fatty acids (SCFAs). However, reduced serum levels of essential fatty acids, vitamins B1 and B3 by HFD were further decreased by both inulin supplementations. ML inulin can prevent HFD‐induced obesity and the associated metabolic disorders, and may be used as novel gut microbiota modulator to prevent HFD‐induced gut dysbiosis and metabolic disorders.