Single crystal 6H-SiC wafers with 4° off-axis [0001] orientation were irradiated with carbon ions and then annealed at 900 °C for different time periods. The microstructure and surface morphology of these samples were investigated by grazing incidence X-ray diffraction (GIXRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Ion irradiation induced SiC amorphization, but the surface was smooth and did not have special structures. During the annealing process, the amorphous SiC was recrystallized to form columnar crystals that had a large amount of twin structures. The longer the annealing time was, the greater the amount of recrystallized SiC would be. The recrystallization volume fraction was accorded with the law of the Johnson–Mehl–Avrami equation. The surface morphology consisted of tiny pieces with an average width of approximately 30 nm in the annealed SiC. The volume shrinkage of irradiated SiC layer and the anisotropy of newly born crystals during annealing process produced internal stress and then induced not only a large number of dislocation walls in the non-irradiated layer but also the initiation and propagation of the cracks. The direction of dislocation walls was perpendicular to the growth direction of the columnar crystal. The longer the annealing time was, the larger the length and width of the formed crack would be. A quantitative model of the crack growth was provided to calculate the length and width of the cracks at a given annealing time.