A new 3D-XRF instrument was developed with a fine-focus X-ray tube. The depth resolution of the developed instrument was 13.7 µm at the energy of Au Lβ (11.4 keV). Compared with the previous 3D-XRF instrument developed in the author's research group, the depth resolution was improved by a factor of 3–4. A small dependence of depth resolution on X-ray energy was also confirmed for the new instrument. The depth resolution was varied from 22.6 µm to 13. 7 µm for an energy range from 5.4 keV to 11.4 keV, respectively. A few layered materials were measured by two (previous and new) 3D-XRF instruments. As expected, the new 3D-XRF instrument gave a depth profile with a high-resolution. In addition, a 3D-structured material was proposed and developed to evaluate the 3D-imaging performance. The material consisted of two cylindrical patterns of Au having a micrometre-scale structure. Elemental imaging performance was compared by using this 3D-structured material for two different 3D-XRF instruments.