In this study, we investigated the effects of a newly synthesized α-galacto-oligosaccharide mixture (α-GOSg), 0.5% in drinking water, on high-fat/western-style diet (HFWD)-induced metabolic abnormality in mice in a study of 13 weeks. Raffinose family oligosaccharides (RFOs) were included as a comparison. Mice treated with α-GOSg had significantly lower body weight and body fat (p < 0.05), while RFOs were less effective. Both α-GOSg and RFOs significantly reduced serum levels of total cholesterol and low-density lipoprotein cholesterol, alanine aminotransferase and liver lipids. However, only α-GOSg significantly decreased the histopathological score for liver steatosis and downregulated hepatic fatty acid synthesis gene acetyl CoA carboxylase-α. α-GOSg also significantly reduced the content of bile acids in the small intestine and significantly increased the abundance of gut Bifidobacterium and decreased the abundance of Clostridium leptum. These actions are proposed to be key mechanisms contributing to the beneficial health effects of α-GOSg.