In this study, high-energy x-ray nanotomography (nano-computed tomography, nano-CT) based on full-field x-ray microscopy was developed. Fine two-dimensional and three-dimensional (3D) structures with linewidths of 75 nm–100 nm were successfully resolved in the x-ray energy range of 15 keV–37.7 keV. The effective field of view was ∼60 µm, and the typical measurement time for one tomographic scan was 30 min–60 min. The optical system was established at the 250-m-long beamline 20XU of SPring-8 to realize greater than 100× magnification images. An apodization Fresnel zone plate (A-FZP), specifically developed for high-energy x-ray imaging, was used as the objective lens. The design of the A-FZP for high-energy imaging is discussed, and its diffraction efficiency distribution is evaluated. The spatial resolutions of this system at energies of 15 keV, 20 keV, 30 keV, and 37.7 keV were examined using a test object, and the measured values are shown to be in good agreement with theoretical values. High-energy x-ray nano-CT in combination with x-ray micro-CT is applied for 3D multiscale imaging. The entire bodies of bulky samples, ∼1 mm in diameter, were measured with the micro-CT, and the nano-CT was used for nondestructive observation of regions of interest. Examples of multiscale CT measurements involving carbon steel, mouse bones, and a meteorite are discussed.