The objective of this study is to investigate the degree of visualization for the macro-, micro-, and nano-structures of the cochlea with x-ray micro-CT based on a cone-beam geometry for rats. This study will provide a basic criterion to compare the visual images obtained from other techniques. Before obtaining the visual images, the hearing thresholds were obtained with auditory brainstem responses (ABR). A x-ray micro CT based on a cone-beam geometry for a small animal was used for examining the macro-, micro-, and nano-structures of the cochlea in rats. X-ray micro CT provided a clear depiction of the basal, middle, and apical cochlear turns. X-ray micro CT allows visualizing the macro-structures of the cochlea. However, it did not well depict the micro- and nano-structures of the cochlea. The present study was the first attempt to visualize the macro-structures of the cochlea with x-ray micro CT based on a cone-beam geometry for rats. To visualize the micro- and nano-structures of the cochlea, optimal parameter values of x-ray micro CT should be found and many factors such as signal-to-noise ratio, resolution, image averaging, pixel, pixel number, pixel value, exposure time, and binning should be properly considered.