Conventional machining technologies such as a milling process have limitations in accuracy to fabricate microstructures. Deep X-ray lithography using the synchrotron radiation is a promising micromachining process with an excellent accuracy, whereas there are difficulties in the fabrication of multi-layered structures. Therefore, it is mainly used for fabricating simple mono-layered microstructures with a high aspect ratio. In this study, a novel technology for fabricating multi-layered microstructures is proposed by combining two processes. In advance, an X-ray resist material is cut and machined into various shapes and heights by the micro milling process. Subsequent X-ray irradiation process facilitates the fabrication of multi-layered microstructures. The proposed technology can overcome the limitation of the pattern accuracy in conventional milling process and the difficulty of the multi-layered machining in x-ray process. The usefulness of the proposed technology is demonstrated in this study by applying the technique in the realization of various multi-layered microstructures.