We have completed a system that can achieve both deep x-ray lithography and submicron x-ray lithography with a single beamline by introducing the combination of x-ray plane and cylindrical mirrors. This x-ray lithography system can provide a large-scale microfabrication processing with 210 × 300 mm2 (A4 size). To exploit multiscale lithography, the beamline has a beam transport vacuum duct with a two-stage stacked structure and a 5-axis stage. This two-stage stacked structure allows us to fabricate both micron scale structures with high aspect ratios and submicron scale structures using the same beamline. In addition, x-ray imaging and computer tomography (CT) system are connected to the x-ray lithography system for nondestructive inspection and evaluation of the fabricated microstructures. The x-ray imaging system constructed this study has a relatively low energy range of x-ray energy in the beamline, which is in the range of 2–15 keV or less. Therefore, relatively good absorption contrast can be obtained for plastic materials, biomaterials, and the like. Since nondestructive imaging of the processed shape by x-ray lithography is possible, it is a very useful system in processing and evaluation can be performed simultaneously. This system also enables us to obtain the live images with keeping the creature alive in liquid using an indirect x-ray imaging system which converts x-ray images to visible light images through the fluorescent plate.