We propose a tomographic method using X-ray Talbot interferometry for mapping three-dimensional distribution of parameters characterizing microstructures, which are typically of the order of μm in size and cannot be resolved by the imaging system, in a sample. In the method we use reduction in fringe visibility, which is due to such unresolvable microstructures, of moiré images obtained in the interferometry. We applied this method to a sample of melamine sponge containing chloroprene rubber. We performed tomographies at several Talbot orders and obtained the dependencies of the reconstructed values on the Talbot order for voxels. The parameters obtained by the least-squares fitting to the dependencies were consistent with those previously obtained from projection images for each material. Our approach provides three-dimensional structural information on unresolvable microstructures in real space, which is only accessible through the ultra-small-angle X-ray scattering (USAXS) in reciprocal space, and is expected to be broadly applicable to material, biological, and medical sciences.