OBJECTIVEPrevious researches have demonstrated that patients with subcortical ischemic vascular disease (SIVD) exhibited brain structure abnormalities. However, the cortical macrostructural and microstructural characteristics and their relationship with cognitive scores and gene expression in SIVD patients remain largely unknown.METHODSThis study collected 3D-T1 and diffusion tensor imaging data from 30 SIVD patients with cognitive impairment (SIVD-CI) and 32 normal controls. The between-group comparative analyses of cortical thickness, area, volume, local gyrification index (LGI), and mean diffusivity (MD) were conducted with a general linear model. Moreover, the associations between the significant neuroimaging values and the cognitive scores and gene expression values from Allen Human Brain Atlas database were evaluated using partial least squares regression and partial correlation analysis.RESULTSSIVD-CI patients showed significant decreases in cortical thicknesses across 18 regions, cortical volumes across three regions, and cortical LGI across five regions, as well as significant increases in cortical MD across five regions (P < 0.05). The significantly reduced cortical thicknesses of the right insula, left superior temporal gyrus, left central anterior gyrus, and left caudal anterior cingulate cortex, as well as the significantly reduced cortical LGI in left caudal anterior cingulate cortex, were significantly positively correlated with different cognitive scores (P < 0.05). Furthermore, the abnormal cortical structural indicators were found to be significantly related to nine risk genes (VCAN, APOE, EFEMP1, SALL1, BCAN, KCNK2, EPN2, DENND1B and XKR6) (P < 0.05).CONCLUSIONSThe specific cortical structural damage may be related to specific cognitive decline and specific risk genes in SIVD-CI patients.