Blueberry anthocyanins (VA) and blackberry anthocyanins (RA) showed benefits on metabolic syndrome (MS) induced by high-fat diet in mice. In this study, we investigated whether the therapeutic effects of VA and RA were achieved by the gut microbiota regulation and whether these effects could be replicated through fecal microbiota transplantation (FMT) using the high-fat diet caused MS model in pseudo-germ-free (PGF) mice. The results demonstrated that the beneficial effects of VA and RA on MS, including reducing body weight gain and fat accumulation, improving glucose and lipid metabolism, and mitigating intestinal barrier damage, were attributed to the gut microbiota and could be replicated by FMT. 16S rRNA sequencing analysis suggested that FMT from donor mice supplemented with VA and RA could regulate the gut microbiota composition. Particularly, FMT from RA supplemented mice displayed the potential to restore the diversity of gut microbiota and the ratio of Firmicutes to Bacteroidetes. Meanwhile, FMT from VA supplemented mice appeared to exert its effects by selectively influencing specific gut microbiota, such as the genus Akkermansia. Furthermore, our analysis identified 10 common differential ASVs among groups compared to HFD-HFD group. Notably, ASV_36450 was negatively associated with metabolic parameters, suggesting that Lactobacillus might be the potential bacteria in regulating MS. Overall, our study demonstrated that FMT from VA and RA supplemented mice could ameliorate MS induced by high-fat diet in mice through regulating specific gut microbiota.