Previous studies have revealed that age‐related hearing loss (AHL) in Cdk5 regulatory subunit‐associated protein 1 (Cdk5rap1)‐knockout mice is associated with pathology in the cochlea. Here, we aimed to identify mitochondrial alterations in the cochlea ofCdk5rap1‐knockout mice with AHL. Mitochondria in the spiral ganglion neurons (SGNs) and hair cells (HCs) were normal despite senescence; however, the mitochondria of types I, II, and IV spiral ligament fibrocytes were ballooned, damaged, and ballooned, respectively, in the stria vascularis. Our results suggest that the accumulation of dysfunctional mitochondria in the lateral wall, rather than the loss of HCs and SGNs, leads to the onset of AHL. Our results provide valuable information regarding the underlying mechanisms of AHL and the relationship between aberrant tRNA modification‐induced hearing loss and mitochondrial dysfunction.