Probiotics can prevent obesity and related metabolic complications. In our study, the protective effect and molecular mechanism of Lactobacillus rhamnosus JL1 (separated from the feces of healthy infants) on high-fat diet mice were investigated. After 10 weeks of dietary intervention with L. rhamnosus JL1 intervention, the body weight of the JL1 group (23.78 g) was significantly lower than that of the HFD group (26.59 g, p < 0.05) and the liver index was reduced. Serum biochemical analysis showed that the TC, TG and LDL-C contents of JL1 group mice were significantly decreased (p < 0.05). Histological images of the mice livers showed that the degree of lipid action and damage of hepatic cells were improved. L. rhamnosus JL1 activated the AMPK pathway, and reduced the gene expression of PPAR-γ, LXR-α and SREBP-1C. In addition, the protein expression of PPAR-γ and LXR-α were reduced. After dietary intervention with L. rhamnosus JL1, the concentration of acetic acid, propionic acid, and butyric acid were increased significantly, especially the concentration of butyric acid, which was 63.16% higher than that of the HFD group (p < 0.05). In conclusion, this study provided a theoretical reference for the development and application of probiotics derived from healthy infant feces in health products and functional foods.