High-oleic acid peanut oil (HOPO) and extra-virgin olive oil (EVOO) have been reported previously to have an attenuating effect on metabolic syndrome (MS). This study aimed to evaluate the metabolic effect of HOPO and EVOO supplementation in attenuating MS and the role of gut microbiota in regulating the metabolic profile. Sprague-Dawley rats were continuously fed with a normal diet, high-fructose and high-fat (HFHF) diet, HFHF diet containing HOPO, or a HFHF diet containing EVOO for 12 weeks. The metabolomics profiles of feces and serum samples were compared using untargeted metabolomics based on UPLC-Q/TOF-MS. Partial Least Squares Discriminant Analysis (PLS-DA) was used to identify the potential fecal and serum biomarkers from different groups. Correlation between gut microbiota and biomarkers was assessed, and pathway analysis of serum biomarkers was conducted. Differences in metabolic patterns in feces and serum were observed among different groups. There were 8 and 12 potential biomarkers in feces and 15 and 6 potential biomarkers in serum of HOPO group and EVOO group, respectively, suggesting that HOPO and EVOO supplementation mainly altered amino acids, peptides, and their analogs in feces and serum. The branched-chain amino acids (BCAAs) biosynthesis pathway was identified as a major pathway regulated by HOPO or EVOO. This study suggests that HOPO and EVOO supplementation ameliorate diet-induced MS, mainly via modulation of the BCAAs biosynthesis pathway.