To elucidate the nature of the mechanical properties of rubber composite, it is necessary to investigate the 3D structure of polymers and fillers in rubber composite over a wide-size scale. We have utilized ultra-small-angle X-ray scattering to observe changes in the aggregate/agglomerate structure of nanoparticles in uniaxially stretched rubber.^{1), 2)} However, real-space 3D structural information cannot be directly obtained with a scattering technique. Therefore, the development of a real-space microscopy technique is required. X-ray imaging techniques have also been developed in association with advances in synchrotron X-ray technology. The advantages of X-ray imaging include a wider field of view, sub-micron-level spatial resolution and less damage to the specimen. In this study, the 3D structure of spherical silica particles and polymers in rubber composite was visualized with a higher spatial resolution using a Zernike-type phase contrast X-ray microtomography. This method improved the contrast of images and gave us an opportunity to investigate a detailed 3D-submicron scale configuration of fillers and polymers with a wide field of view. This method was proven to be a powerful tool to obtain the 3D structural configuration of soft materials.