Silicon carbide is one of the most studied materials for core components of the next generation of nuclear plants (Gen IV). In order to overcome its brittle properties, materials with nanometric grain size are considered. In spite of the growing interest for nano-structured materials, only few experiments deal with their behaviour under irradiation. To assess and predict their evolution under working conditions, it is important to characterize their microstructure and structure. To this purpose, we have studied microcrystalline and nanocrystalline samples before and after irradiation at room temperature with 4 MeV Au ions. In fact, it is well established that such irradiation conditions lead to amorphisation of the material, which can be restored after annealing at high temperature. We have performed isochronal annealings of both materials to point out the characteristics of the healing process and eventual differences related to the initial microstructure of the samples. To this purpose Grazing Incidence X-Ray Diffraction has been performed to determine the microstructure and structure parameters. We observe the amorphisation of both samples at similar doses but different annealing kinetics are observed. The amorphous nanocrystalline sample recovers its initial crystalline state at higher temperature than the microcrystalline one. This effect is clearly related to the initial microstructures of the materials. Therefore, the grain size appears as a key parameter for the structural stability and mechanical properties of this ceramic material under irradiation.