We developed a new X-ray lithography system for the lithographite, galvanoformung and abformung process (LIGA process) using synchrotron radiation at the NewSUBARU facility of the University of Hyogo. The X-ray lithography system can utilize two different energy regions: one is a high-energy region: from 2 keV to 12 keV, and the other is a low-energy region from 1 to 2 keV. Each energy region can be selected in accordance with the size and shape of the desired microstructures. Large-area patterning across an A4-size area was successfully performed with a highly uniform pattern thickness. Furthermore, high-aspect-ratio patterning using a high-X-ray-energy region was also achieved using this X-ray lithography system.