A novel method to generate microstructures and calculate thermal and elastic properties in non-oxide ceramics, namely in Aluminum Nitride (ALN), Silicon Nitride (Si3N4), and Silicon Carbide (SiSiC) is presented. Structural features like dihedral angle (ALN), anisotropic material properties of grains (Si3N4), and multiscale structure (SiSiC) are considered. To ensure that the simulated structures are close to the real materials, several samples of all ceramics were prepared by the artifact-free method of cross section polishing and imaged by scanning electron microscopy (SEM). By image analysis chord lengths, phase fractions, connectivity between grains or elongation of grains were obtained. The same parameters were extracted from 2-dimensional sections of 3-dimensional representative volume elements produced by a structure generator. Structure generation followed closely the structure formation in the real process. It was repeated until close agreement between experimental and theoretical structures was obtained. Then, thermal and mechanical properties were calculated by finite element simulations. The calculated material properties showed good agreement to the obtained experimental data.