The potential health benefit of dietary fiber has attracted considerable attention in recent decades. In this study, the effects of modified dietary fibers (MDF) derived from okara on body composition, fat distribution, serum metabolomic parameters, and fatty acid profiles in mice fed high-fat diets (HFD) were evaluated by nuclear magnetic resonance (NMR)-based metabolic approach. HFD-induced C57BL mice were fed with a diet containing 100 g/kg MDF for 12 weeks. Compared with control mice, MDF-fed mice exhibited less fat and lower body weights, altered serum metabolomic profiles, and distinct fatty acid profiles. The levels of choline, phosphatidylcholine, glycerophosphorylcholine, glucose, lysine, scyllo-inositol, and glutamate for MDF group were higher than those for both CONT and HFD groups. A remarkable reduction of total cholesterol, total triglycerides, omega-6 fatty acids, alanine, citrate, creatine, or succinate was also observable for MDF group compared with HFD group. These findings demonstrated that the intake of MDF derived from okara clearly ameliorated some of the HFD-induced adverse metabolic effects and prevented adipose tissue accumulation.