In this study, we used Surface Based Morphometry (SBM) and Tract-Based Spatial Statistics (TBSS) analysis to investigate the alternation of brain structure in deaf children. The cortical thickness of the deaf group significantly decreased in the left postcentral gyrus, superior parietal lobule, paracentral lobule, precuneus, the right transverse temporal gyri, and the middle temporal gyrus. The left precuneus local gyrification index increased. The fractional anisotropy value of the white matter in deaf children is lower than control group. These findings demonstrated that structural changes in deaf children occurred in both the grey and white matter, and revealed that the neuroplastic changes associated with cross-modal reorganization in the precuneus.