Low protein (LP) diet can reduce feed costs and decrease nitrogen emission. Branched chain amino acids (BCAA), especially leucine, have been shown to influence muscle protein metabolism. Here, we used HPLC-high-resolution MS-based metabolomics approach to investigate the effects of LP diet supplemented with BCAA on metabolome in the muscle of piglets. The 10-21 kg piglets were fed with LP diet supplemented with BCAA. Amino acids (AAs) and metabolomics profiles of plasma, muscle, and liver were analyzed. Free AA profiles of plasma showed increased levels of BCAA. Multivariate analysis showed significant difference in skeletal muscle metabolites among different diet treatment groups, and most of the identified differential compounds were involved in AA metabolism and protein anabolism. These compounds, including alanine, glutamine, sarcosine, ornithine, proline, methionine, and threonine, all increased in the BCAA supplemented group compared with normal protein diet group. Metabolic pathway analysis suggested that BCAA could be converted to nonessential AAs and their metabolites by direct or indirect synthesis under LP diets, which could participate in the muscle protein synthesis or energy metabolism, and ultimately reduced nitrogen emission.