Host gut microbiota dysbiosis occurs for multiple reasons and is often accompanied by chronic inflammation induced by a high-fat-high-sucrose (HFHS) diet and related metabolic disorders. Intervention with probiotics is a novel strategy for amelioration of metabolic syndrome, which is believed to regulate the gut microbiota composition to some extent. We investigated the relationship amongst bifidobacteria treatment, HFHS diet-induced metabolic disorders and the gut microbiota composition. Seven strains of bifidobacteria from four species were individually administered to rats fed a HFHS diet for 12 weeks. Various bifidobacteria strains showed various effects on the recovery of metabolic disorders and gut microbiota dysbiosis, and these effects seemed to be inter- or intra-species specific. Bifidobacterium longum, B. adolescentis and B. bifidum seemed to affect the blood glucose balance, whilst two strains of B. breve showed extremely different effects in this area. However, only one strain of B. longum and the B. adolescentis displayed significant regulation of blood lipid levels. The protective effects of bifidobacteria on the pancreas were strongly correlated with those on blood glucose. Furthermore, the influence of bifidobacteria on gut microbiota dysbiosis also showed a potential relationship with symptoms of metabolic disorders. Of these seven strains, B. adolescentis Z25 displayed an outstanding ability to alleviate metabolic syndrome, including glucose and lipid metabolism disorders, tissue damage and gut microbiota dysbiosis. This strain, coupled with other prebiotics and probiotics, could be used as a potential treatment approach for metabolic syndrome induced by a HFHS diet.