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Fucoidan from Laminaria japonicais an important natural bioactive substance, and low molecular weight fucoidan (L-F) obtained by hydrothermal degradation exhibits better bioavailability. However, the anti-obesity effect of Laminaria japonicafucoidan (FUC) and whether hydrothermal degradation could enhance its activity remained uncertain. The related indicators were therefore determined and compared. According to the results, the molecular weight and glucuronic acid content of FUC were significantly reduced after degradation. Animal experiment results showed that oral administration of 300 mg/kg FUC effectively reduced body weights and serum lipid levels, while these effects of L-F were diminished. Changes in the expression levels of hepatic gene expression showed that FUC inhibited fatty acid synthesis via down-regulation expression of SREBP-1c and FAS, and promoted cholesterol consumption via up-regulation of CYP7A1 and CYP27A1. However, L-F had no significant effect on SREBP-1c and FAS. FUC and L-F also had regulatory effects on gut microbiota, but there were some differences in their specific effects. FUC improved lipid metabolism by regulating gut microbiota such as Colidextribacter, Desulfovibrioand Colidextribacter, so as to play a role in reducing body weight. L-F had weaker regulatory effect on some fat formation related microbes, which resulted in its reduced anti-obesity effect. Summarily, FUC could ameliorate obesity and improve lipid metabolism disorders, but these activities were diminished after hydrothermal treatment, which may connect with the decarboxylation of glucuronic acid and the change in regulatory activity of gut microbiota.