Objective To conduct a comprehensive quantitative evaluation of the primary lesions and secondary damages of the inner ear in the rat model of intratympanic gentamicin injection. Methods Sixteen adult rats were randomly divided into four groups, with 4 rats in each group: a normal control group (8 ears), a group 7 days after single intratympanic injection of gentamicin (40 mg/mL) (8 ears), a group 30 days after single injection of gentamicin (8 ears), and a group 60 days after single injection of gentamicin (8 ears). One ear from each rat was made into flat surface preparation of whole membranous labyrinth to quantitatively evaluate the hair cell density in each sensory epithelial region, while the other ear was sectioned along the sagittal plane of the temporal bone for quantitative evaluation of the density of cochlear and vestibular neurons and the density of their peripheral and central nerve fibers. Results Quantitative analysis of hair cells in the surface preparations of whole membranous labyrinth showed that the extent and severity of hair cell damage were consistent across different observation time points following intratympanic gentamicin injection. This indicated that gentamicin-induced initial destruction of hair cells did not cause significant secondary degeneration of the surviving hair cells. Quantitative analysis of the inner ear nervous system in sagittal temporal bone sections revealed that the peripheral nerve fibers of cochlear and vestibular neurons were almost completely absent 30 days after hair cells death. However, the soma of the inner ear neurons and their central nerve fibers remained unaffected at 30 days after hair cell missing. Significant secondary degeneration of the inner ear neurons and their central nerve fibers did not occur until 60 days after the hair cell loss. Conclusion The degeneration of peripheral nerve fibers of inner ear neurons occurs earlier than the delayed degeneration of neuronal cell bodies and their central nerve fibers after hair cell loss. The early degeneration of peripheral nerve fibers indicates the complete loss of peripheral neural connection due to hair cell loss, while the secondary damage of central nerve fibers provides evidence of the disruption of neural connections between the inner ear and the central nervous system.