As a nontargeted metabolomics approach, we investigated changes in the plasma metabolite levels in a mouse model of obesity induced by a high-fat diet and fermented soybean product diet. We analyzed the plasma samples by using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). In the present study, the animals were divided into four groups according to the diet type; normal fat diet control group (ND), high-fat diet control group (HD), high-fat diet plus 30% cooked soybean power (HD + S), and high-fat diet plus 30% 72-h fermented Cheonggukjang powder (HD + CGJ). To examine the changes in plasma metabolite levels because of high-fat diet feeding, total cholesterol and triglyceride levels were measured. Total cholesterol and triglyceride levels were lower in the HD + S and HD + CGJ groups than in the ND group. According to partial least-squares discriminant analysis (PLS-DA), major metabolites contributing to the discrimination between each group were assigned as lipid metabolites in plasma, e.g., lyso-phosphatidylcholines and phosphatidylcholines. Therefore, diets containing soy-based food products, which are rich sources of isoflavonoids, might be helpful for controlling the lipid metabolism under high-fat diet conditions.