Although the specific location is not clear and its dating is still debated, the Ziyang human fossil has attracted extensive attention from academic circles because it is the first almost complete human skull fossil found after the establishment of the People’s Republic of China. For a long time, the research on the Ziyang skull was limited to only external morphology and measurements using traditional methods. In order to better understand the evolutionary stage of the Ziyang hominid, a high-resolution industrial CT scanner was used to analyze its internal anatomy, and 3D virtual reconstructions of its bone structure, frontal sinus, bony labyrinth, pneumatization of mastoid air cells, and endocast were created and analyzed. CT images of the bone structure shows that the diploë is very thick—much thicker than the outer and inner layers. This supports the previous identification results of the Ziyang individual over 50 years old. The frontal sinus of the Ziyang is in the shape of a leaf, bilaterally located on the inner and upper orbital areas, with surface areas on the left and right of 1780 mm²and 2910mm², respectively. The size and proportion of the Ziyang semicircular canals of the bony labyrinth are different from Neandertals, but are in the ranges of those from Late Pleistocene Homo sapiens and recent modern humans. The pneumatization of mastoid cells was in pneumatic type, and almost occupied the entire mastoid process with pneumatic cavities. Based on the 3D virtual reconstruction of the endocast, the cranial capacity of the Ziyang skull was estimated at around 1250 mL. Although the endocast is small in all measurements, most of the brain morphology as well as the width-height index and the parietal lobe-length index were all within the variation range of modern humans, which are different from those of Homo erectus and Pleistocene archaic humans. The internal anatomy of the Ziyang skull retains a few original features, including the two occipital lobes that are prominently backwardly convex, and the cerebral fossa, which is larger and deeper than the cerebellar fossa. These two features are different from Holocene humans but are similar to Pleistocene early modern humans.