Background and purpose: Previous voxel-based morphometry (VBM) studies have suggested that cortical atrophy is regionally distributed in middle-aged subjects with white matter hyperintense (WMH) lesions. However, few studies have assessed cortical thickness in middle-aged WMH subjects. In this study, we examined cortical thickness as well as cortical morphometry associated with the presence of WMH lesion load in middle-aged subjects. Participants and methods: Thirty-six middle-aged subjects with WMH lesions (WMH group) and without clinical cognitive impairment, and 34 demographically matched healthy control subjects (HCS group) participated in the study. Cortical thickness was estimated using an automated Computational Anatomy Toolbox (CAT12) as the distance between the gray-white matter border and the pial surface. Individual WMH lesions were manually segmented, and WMH loads were measured. Statistical cortical maps were created to estimate differences in cortical thickness between groups based on this cortex-wide analysis. The relationship between WMH lesion loads and cerebral cortical thickness was also analyzed in CAT12. Results: Cortical thickness was significantly lower in the WMH group than in the controls in multimodal integration regions, including the right and left dorsal anterior cingulate cortex (dACC), right and left frontal operculum (fO), right and left operculum parietale (OP), right and left middle temporal gyrus (MTG), and left superior temporal gyrus (STG; P < 0.01, family-wise error (FWE)-corrected). Additionally, cortical thickness was also lower in the recognition regions that contained the right temporal pole (TP), the right and left fusiform gyrus, and the left rolandic operculum (RO; P < 0.01, FWE-corrected). The results revealed that in the left superior parietal lobule (SPL), cortical thickness was higher in the WMH group than in the HCS group (P < 0.01, FWE-corrected). A voxel-wise negative correlation was found between cortical thickness and WMH lesion loads in the right orbitofrontal cortex (OFC), right dorsolateral prefrontal cortex (DLPFC), and right subcallosal cortex (P < 0.01, FWE-corrected). Conclusion: The main findings of this study suggest that middle-aged WMH subjects are more likely to exhibit cortical thinning, especially in multimodal integration and recognition- and motor-related regions. The current morphometry data provide further evidence for WMH-associated structural plasticity.