A methionine-restricted diet (MRD) has been shown to reduce body fat deposition and improve obesity-associated metabolic disorders, with emerging evidence implicating the gut microbiota in mediating these effects. This study investigated the effects and underlying mechanisms of fecal microbiota transplantation (FMT) from MRD mouse donors on body fat deposition in obese mice. Five-week-old male C57BL/6J mice were continuously fed a high-fat diet (HFD, 0.86% methionine + 24% fat) to induce obesity, and then randomly divided into three groups. These groups received FMT from 23-week-old male C57BL/6J mice donors continuously fed with normal diet (0.86% methionine + 4.2% fat), HFD, or MRD (0.17% methionine + 24% fat) for eight weeks, respectively. Our results indicate that FMT from MRD mouse donors reduced body weight, plasma lipid levels, and percentage fat mass. Moreover, FMT from MRD mouse donors elevated the abundance of short-chain fatty acid (SCFA)-producing bacteria while decreasing pro-inflammatory bacteria levels in cecal contents. In addition, systemic metabolic processes were altered, featuring heightened SCFA production and enhanced energy metabolism. FMT from MRD mouse donors further facilitated fat catabolism, inhibited fat anabolism, and decreased lipid levels and lipid accumulation in liver. Meanwhile, FMT from MRD mouse donors also promoted fat browning, decreased adipocyte volume, and reduced fat deposition in adipose tissues. These findings underscore the potential of FMT from MRD mouse donors to improve the gut microbiota and reduce body fat deposition in obese mice. Importantly, our results elucidate that MRD intervention in obesity is, in part, mediated by regulating intestinal microbial composition.