Using computed tomography, we examined the surface and internal morphologies of the upper face of people living on the Ryukyu Islands and mainland Japanese, focusing on the nasal root protrusion and eyeball position. The results showed that the nasal root protrusion on the surface was influenced by a combination of changes in both hard and soft tissues, such as skeletal nasal protrusion, eyeball recession, and skin thickness. The eyeball position became more posterior as the orbital cavity height and depth increased. Compared with people originating from mainland Japan, Ryukyu Islanders had a more prominent nasal root at both surface and skeletal levels, and a lower orbital rim relative to its internal height. However, a significant difference in the eyeball position and skin thickness was not detected. Therefore, the skeletal nasal root protrusion, not soft tissue configuration, is likely to account for the difference in the surface nasal root protrusion between the two populations. These findings will contribute to a better understanding of the association between hard and soft tissue configurations and the diversification of human facial features at the individual and population levels.