The structural deformations in Si/SiGe system during thermal annealing were investigated by means of atomic force microscope (AFM) and high-resolution X-ray diffraction (HRXRD). The (004) rocking curve measurements showed that the obvious fringes of rocking curve obtained from pre-annealing sample were faded out gradually and disappeared completely with increasing the annealing temperature, which indicated that the abrupt Si/SiGe interface was destroyed gradually. The analyses of the peak broadening and relative position of the SiGe epilayer with respect to the Si substrate in high-resolution reciprocal space map (HRRSM) measurements described clearly the formation of mosaic structure in Si/SiGe system. The inner deformation induced the surface corrugate, known as crosshatch morphologies, which was analyzed by AFM measurements.