Disrupted white matter structure has been established in patients with diffuse axonal injury (DAI), but morphological changes in gray matter and local intrinsic activity in the short and midterm (before 6 months) have not been documented in DAI patients. We hypothesized that regionally selective atrophy observed in deep gray matter in the short-term and mid-term periods in patients with mild-to-moderate DAI, local atrophy, and/or dysfunction would be related to clinical characteristics. We evaluated the changes in regional density and synchronization in 18 DAI patients separately using Diffeomorphic Anatomical Registration through Exponentiated Lie algebra-enhanced voxel-based morphometry and regional homogeneity (ReHo). Compared with the controls, DAI patients showed a decreased density in the bilateral thalami and decreased ReHo values in the ventral anterior and ventral lateral nuclei of the bilateral thalami. Pearson's correlation analysis showed that decreased density in the bilateral thalami was correlated negatively with time since injury and decreased ReHo values in the ventral anterior and ventral lateral nuclei of the bilateral thalami were associated with a worsened motor assessment scale. These findings suggest that mild-to-moderate traumatic DAI within the short and midterm could lead to thalamic atrophy and that dysfunction in the bilateral thalami is associated with declining motor function. This study could potentially provide complementary evidence as an important element in longitudinal studies.