Toxic effect of heavy metal cadmium (Cd) on fish kidneys had been reported. Mitochondrion is an important organelle for maintaining kidney function, while its role in Cd-induced kidney injury in common carp remained unclarified. In this experiment, we established a poisoning model of common carp with Cd exposure (0.26 mg/L) for 15, 30, and 45 days. Serum biochemistry determination, histological observation, TUNEL assay, qRT-PCR, Western blot, and integrated biomarker response (IBR) were applied to assess the nephrotoxicity of Cd to common carp. Our results displayed that Cd exposure increased the levels of serum biochemical indexes (UREA, CRE, and UA), indicating kidney injury. We further revealed via histological observation that Cd damaged structural integrity of kidneys, as evidenced by renal glomerulus and renal tubular injury, hallmark phenotypes of apoptosis, and mitochondrial damage, suggesting that mitochondria damage and apoptosis were involved in Cd-induced kidney injury. Moreover, Cd exposure decreased ATPase (Na/K-ATPase, Ca-ATPase, Mg-ATPase, and CaMg-ATPase) activities as well as PGC-1a and Mfn2 levels, while increased Drp1 and PINK1 levels as well as LC3-II/LC3-I ratio, which indicated that Cd-impaired renal energy metabolism was related to mitochondrial dysfunction. Additionally, we found that Cd induced oxidative stress (abnormal levels of SOD, CAT, GPX, MDA, and HO) in kidneys, which was involved in triggering mitochondrial dysfunction and further impairing mitochondrial energy metabolism. Moreover, the occurrence of mitochondria-dependent apoptosis was found after Cd-exposure in common carp kidneys, as indicated by enhanced levels of Bax, CytC, APAF1, Caspase-9, and Caspase-3, while declined level of Bcl-2. Subsequently, we confirmed a time-dependent nephrotoxicity of Cd to common carp via IBR assessment. In conclusion, Cd induced time-dependent nephrotoxicity in common carp via mitochondrial pathway. This mitochondria-oriented study shed light on underlying mechanisms of Cd-induced renal pathologies and provided a theoretical basis for evaluating Cd toxicity to aquatic organisms.