According to the World Health Organization (WHO), a growing number of 0.5 billion people currently suffer from disabling hearing loss (HL). While causes of HL are diverse, it mainly originates in dysfunctions of the inner ear. Recent improvements in light sheet fluorescence microscopy allow nanometric examination of the whole intact cochlea in immunohistochemistry. These findings may help to identify and quantify disease mechanisms on a new scale and aid in the development of new treatment options for patients with severe HL. In this study, we assess the nano-architecture of the cochlea using a cutting-edge, custom-built cleared tissue light sheet microscope (CTLSM), which provides an isotropic resolution of 0.8µm with unprecedented clarity and detail. Native and genetically modified mouse cochleae were decalcified, immunolabelled, and cleared using an optimized iDisco+ protocol. For quantification of cochlear structures, such as spiral ganglion neurons (SGNs) and auditory hair cells, we establish a deep learning-based algorithm called StarDist. The high isotropic resolution of the CTLSM allows for precise analysis of SGN density and subtypes in the cochlea. For the first time, we can now resolve fine subcellular structures and map inner hair cells and their synapse distributions throughout the whole intact cochlea. The generation of robust immunolabelling protocols, together with the innovative CTLSM, enables nanoscale analysis of cochlear architecture and distinct fluorescence patterns on a cellular to subcellular level. This will contribute to the understanding of hearing, its disease mechanisms, as well as to hearing restoration and the development of future auditory prostheses.