Abstract: Onychostoma sima is a precious economic species with its delicious and nutritious meat in the Wujiang River basin. However, there are few research on the stocking density in recirculating aquaculture systems. In order to improve the breeding benefits of O. sima, a density experiment was conducted to investigate the effects of different stocking densities on the growth performance, biochemical composition, intestinal health, and muscle metabolites of juvenile O. sima in a recirculating aquaculture system, and to determine the optimal stocking density. A total of 3900 juvenile fish with an average body weight of 1.75—1.79 g were selected to three density groups: low density (LD, 40 fish/m³, medium density (MD, 160 fish/m³), and high density (HD, 320 fish/m³), with three replicates per treatment, in a 10-week growth experiment. The results showed that: 1) The final average weight, daily weight gain, specific growth rate of body weight, final total length, daily length gain, and specific growth rate of body length decreased significantly with increasing stocking density (P<0.05), while no significant differences between the LD and MD groups (P>0.05); 2) The content of methionine in the HD group was significantly higher than that in the LD and MD groups (P<0.05), while no significant difference were observed between the LD and MD groups (P>0.05). The amino acid in the MD group was more balanced, indicating the highest nutritional value; 3) High density stress significantly inhibited the activity of intestinal lipase and amylase (P<0.05); 4) The activity of superoxide dismutase (SOD), glutathione peroxidase (GPX), and total antioxidant capacity (T-AOC) in the intestinal tract of the HD group were significantly higher than those in the LD and MD groups (P<0.05), while there was no significant difference between the LD and MD groups (P>0.05); 5) The stocking density did not significantly affect the ACE, Chao1, Simpson, or Shannon indices of the intestinal tract in any treatment group(P>0.05). Based on growth performance and intestinal health indicators, the suitable stocking density of juvenile O. sima in a recirculating aquaculture system is 160 ind./m³. Untargeted metabolomics identified 21 differential metabolites in muscle between the LD and HD groups, including 10 upregulated and 11 downregulated metabolites. Under high-density conditions, alterations in differential metabolites such as lipids, amino acids, and organic acids were primarily associated with propionate metabolism, lysine degradation, alanine/aspartate/glutamate metabolism, and fatty acid degradation, which may be the primary factors contributing to growth inhibition.