Branched-chain amino acids (BCAAs) are reduced in various protein restricted models, while the detailed role of BCAAs in protein restricted response is still obscure. Thus, the current study mainly investigated the amino acid metabolism in protein restricted piglets and the effects of BCAA balance in a low-protein diet on growth performance, amino acid metabolism, intestinal structure, and gut microbiota with focus on which BCAAs contributed to the protein restricted response. The results showed that protein restriction increased serum Ser, Thr, Ala, Lys, and Trp but reduced His, Cys, Val, and Ile levels. Intestinal amino acid transporters mainly mediated the mechanism of amino acid uptake. The BCAA balance refreshed the serum BCAA pool, which further improved growth performance in protein restricted piglets. Leu, Val, and Ile balances increased serum BCAA concentrations, respectively, and Leu and Val but not Ile enhanced the feed intake and weight gain in protein restricted piglets. In addition, protein restriction impaired the villus structure and increased the number of goblet cells in the ileum. Also, gut microbiota (Spirochaetales, Gammaproteobacteria, Lactobacillales at the order level) were altered in protein restricted pigs, while the BCAA balance markedly improved Gammaproteobacteria, Lactobacillales, and Aeromonadales proliferation, which might mediate growth promotion and amino acid metabolism. In conclusion, protein restriction markedly affected the host amino acid metabolism (i.e., Ser, Thr, Lys, His, BCAAs). The BCAA balance (especially for supplementation with Leu and Val) improved the amino acid metabolism, growth performance, and gut microbiota communities.