High-fat diet (HFD) promotes the imbalance of gut microbiota, contributing to the development of metabolic disorders. Pomegranate juice (PJ) and inulin, as dietary polyphenol and dietary fiber respectively, have been reported to ameliorate diet-induced gut microbiota dysbiosis and metabolic disorders. However, the combined effect of PJ and inulin on HFD-induced metabolic disorders has not been elucidated. In current study, we found that the combination of PJ and inulin prevent HFD-induced obesity, dyslipidemia, and gut microbiota dysbiosis. Moreover, the fecal levels of short-chain fatty acids (SCFAs) produced by inulin were increased after inulin combined with PJ. The levels of pomegranate polyphenol metabolites produced by PJ were also increased after PJ combined with inulin, especially pharmacokinetic analysis showed that the presence of inulin enhance the absorption level of urolithin A. Fecal metabolomic analysis found that PJ combined with inulin alter the metabolic status compared with PJ. It was also showed that the levels of SCFAs and pomegranate polyphenol metabolites among groups were correlated with gut microbiota and metabolic disorders indicators. Our results suggested that PJ combined with inulin prevent HFD-induced metabolic disorders, which may be attributed to the promotion of mutual metabolic transformation and absorption of PJ and inulin by gut microbiota.