Background The experiment was conducted to evaluate the effects of different stocking densities on the trachea barrier and its plasma metabolic profile of finishing broilers.Methods One thousand four hundred and forty 22-day-old Lingnan Yellow feathered broilers were randomly allotted to five different stocking density groups (8, 10, 12, 14, and 16 birds per m2). Each group consisted of three replicates.Results A markedly increased in IL-1β and IL-10 concentrations were observed in 16 birds per m2 treatment group than the groups of 8 and 10 birds per m2 (P < 0.05), but there was no significant difference in IL-4 content among five treatments (P > 0.05). 16 birds per m2 (high stocking density group, HSD) treatment group significantly increased the trachea mucosa thickness than 10 birds per m2 (control group, CSD). HSD group exhibited lower expression of claudin1 and higher muc2 and caspase3 than those in the CSD group. In addition, a total of 10 metabolites were identified at higher (P < 0.05) concentrations, while 7 metabolites were identified at lower (P < 0.05) concentrations in the HSD treatment as compared with the CSD group. Most of these potentially diagnostic biomarkers were involved in substance synthesis and energy metabolism. Further metabolic pathway analysis revealed that pentose and glucuronate interconversions along with pentose phosphate pathway were the most relevant and critical pathway identified from these two groups. The activated pathway may partially interpret the metabolic level to alleviate the adverse effects of stress which caused by high-stocking density in broilers.Conclusions In summary, this study can improve our understanding of the harmful effects of high-stocking density on the trachea barrier and identify two metabolic pathways that may be associated with high-stocking density-induced metabolic disorders in broilers.