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The role of inulin in alleviating obesity-related disorders has been documented; yet, its underlying mechanisms still need to be further investigated. This study attempted to elucidate the causative link between the gut microbiota and the beneficial effect of inulin on obesity-related disorders via transferring the fecal microbiota from inulin-dosed mice to high-fat diet (HFD)-induced obese recipient mice. The results show that inulin supplementation can decrease body weight, fat accumulation, and systemic inflammation and can also enhance glucose metabolism in HFD-induced obese mice. Treatment with inulin reshaped the structure and composition of the gut microbiota in HFD-induced obese mice, as characterized by increases in the relative abundances of <i>Bifidobacterium</i> and <i>Muribaculum</i> and decreases in <i>unidentified_Lachnospiraceae</i> and <i>Lachnoclostridium</i>. In addition, we found that these favorable effects of inulin could be partially transferable by fecal microbiota transplantation, and <i>Bifidobacterium</i> and <i>Muribaculum</i> might be the key bacterial genera. Therefore, our results suggest that inulin ameliorates obesity-related disorders by targeting the gut microbiota.