Background: Copper (Cu), a common feed additive in diets for animals, is effective in improving growth performance and feed efficiency. However, excessive intake of Cu can cause toxic effects. Kidney is the main target organ of Cu, but the relationship between Cu-induced nephrotoxicity and its metabolic process remains unclear.Results: For deeply investigating the nephrotoxicity induced by Cu, a total of 240 broiler chicks were fed with different contents of Cu (11, 110, 220, and 330 mg/kg Cu) for 49 d in this study (60 chicks per group). The results of TUNEL staining showed that Cu could induce apoptosis in kidney with increasing of TUNEL-positive cells. Additionally, a total of 62 differential metabolites were detected by liquid chromatography-mass spectrometry (LC-MS), and mainly enriched in the metabolic pathways including riboflavin metabolism, glutathione metabolism, sphingolipid metabolism, and glycerophospholipid metabolism, which were closely related to mitochondrial metabolism. Meanwhile, the decrease of mitochondrial membrane potential, impairment of mitochondrial respiratory function, and the increase of mitochondrial membrane permeability indicated that renal mitochondria were damaged by excess Cu. Furthermore, the increase of mRNA and protein levels of Drp1, Bax, Bak-1, CytC, Caspase-3/cleaved Caspase-3 and the decrease of mRNA and protein levels of OPA1, Mfn1, Mfn2, and Bcl-2 confirmed that Cu could induce mitochondria-mediated apoptosis in kidney.Conclusions: These results highlighted that mitochondrial metabolism could be considered as an important factor in influencing Cu toxicity, which for further demonstrating that Cu could induce mitochondria-mediated apoptosis in kidney of broilers.