This study investigated the therapeutic effects on metabolic syndrome (MetS) and the impact on the intestinal barrier and gut microbiota of Fu brick tea aqueous extracts (FTE) on MetS in rats fed with a high-fat diet (HFD). Here, the results showed that FTE supplement significantly reduced HFD-induced weight gain, adiposity, dyslipidemia, fasting blood glucose (FBG) increment, and non-alcoholic fatty liver disease (NAFLD). Moreover, FTE supplement resulted in a decline in lipopolysaccharide (LPS) level and attenuation of colonic inflammation and oxidative stress to protect the intestinal barrier function. FTE supplement also maintained the intestinal barrier integrity by improving histological appearance and promoting ZO-1, Occludin, and Claudin-1 protein expression levels. Meanwhile, FTE supplement alleviated the gut microbiota dysbiosis by enhancing the Firmicutes/Bacteroidetes (F/B) ratio and stimulating the colonization of probiotic bacteria such as Akkermansia, Lactobacillus, Adlercreutzia, and Bacteroides. These findings collectively suggest that Fu brick tea could alleviate MetS and MetS-associated traits with the mechanism relevant to the protection of intestinal barrier and gut microbiota regulation.