An X-ray phase tomographic microscope that can quantitatively measure the refractive index of a sample in three dimensions with a high spatial resolution was developed by installing a Lau interferometer consisting of an absorption grating and a π/2 phase grating into the optics of an X-ray microscope. The optics comprises a Cu rotating anode X-ray source, capillary condenser optics, and a Fresnel zone plate for the objective. The microscope has two optical modes: a large-field-of-view mode (field of view: 65 μm × 65 μm) and a high-resolution mode (spatial resolution: 50 nm). Optimizing the parameters of the interferometer yields a self-image of the phase grating with ∼60% visibility. Through the normal fringe-scanning measurement, a twin phase image, which has an overlap of two phase image of opposite contrast with a shear distance much larger than system resolution, is generated. Although artifacts remain to some extent currently when a phase image is calculated from the twin phase image, this system can obtain high-spatial-resolution images resolving 50-nm structures. Phase tomography with this system has also been demonstrated using a phase object.