Nutritional strategies to reduce dietary protein without impairing growth are essential in modern poultry production, as inadequate supply disrupts bone integrity, intestinal function, and nutrient utilization. The present study aimed to investigate the effects of using different levels of branched-chain amino acids (BCAA) in low crude protein (CP) diets on performance, skeletal development, intestinal morphology, and expression of genes related to bone metabolism, tight junction proteins, and amino acid transporter in broiler chickens. A total of 480 one-day-old male and female broiler chicks of the Ross 308 strain were used in a completely randomized design with 4 treatments and 6 replications. The experimental diets included a standard protein diet (NCP), a diet with 10% less protein than the standard (LCP), an LCP diet with 10% more BCAA than the requirement (LCP+10BCAA), and an LCP diet with 20% more BCAA than the requirement (LCP+20BCAA). Supplementation with BCAA at 10 and 20% levels improved body weight gain compared to the LCP treatment (P=0.03). The inclusion of 20% more BCAA than the requirements of the Ross strain in LCP diets increased tibial weight, strength, ash, and calcium content (P<0.05). The muscularis layer thickness was markedly greater in both BCAA-supplemented groups compared to NCP and LCP (P=0.001). However, villus height and villus surface area in broilers of the LCP + 20BCAA group were significantly higher than those of birds in the NCP, LCP, and LCP + 10BCAA groups (P<0.05). The mRNA expression of RUNX-2, BGLAP, and BMP-2 genes was significantly increased in both LCP + 10BCAA and LCP + 20BCAA groups compared with LCP and NCP (P<0.05). CLDN-1, ZO-1 and MUC-2 expression was significantly upregulated in BCAA-supplemented groups compared with NCP and LCP (P<0.05). SLC3A1 expression was significantly decreased in the LCP group compared to other groups (P=0.001). These findings highlight BCAA supplementation as a promising nutritional strategy to mitigate the adverse effects of protein restriction, thereby supporting broiler growth through coordinated improvements in skeletal health, intestinal structure, and nutrient utilization at the molecular level.