Optical coherence tomography (OCT) has advanced significantly over the past two decades and is currently used extensively to monitor the internal structures of organs, particularly in ophthalmology and dermatology. We used ethylenediamine tetra-acetic acid (EDTA) to decalcify the bony walls of the cochlea and investigated the inner structures by deep penetration of light into the cochlear tissue using OCT on a guinea pig model of endolymphatic hydrops (EH), induced by surgical obliteration of the endolymphatic duct. The structural and functional changes associated with EH were identified using OCT and auditory brainstem response tests, respectively. We also evaluated structural alterations in the cochlea using three-dimensional reconstruction of the OCT images, which clearly showed physical changes in the cochlear structures. Furthermore, we found significant anatomical variations in the EH model and conducted graphical analysis by strial atrophy for comparison. The physical changes included damage to and flattening of the organ of Corti—evidence of Reissner's membrane distention—and thinning of the lateral wall. These results indicate that observation of EDTA-decalcified cochlea using OCT is significant in examination of gradual changes in the cochlear structures that are otherwise not depicted by hematoxylin and eosin staining.