Although lacunar infarcts are focal lesions, they may also have more widespread effects. A reduction in cortical thickness in the remote cortex after lacunar infarcts has been detected by structural imaging; however, its underlying microstructural changes are yet to be elucidated. This study aimed to investigate the effects of lacunar infarcts on the microstructural abnormalities associated with cortical thickness reduction in the remote cortex. Thirty-seven patients with chronic lacunar infarcts were included. Brain structural magnetic resonance images (MRIs) and diffusion tensor images were acquired. We constructed the white matter tracts connecting with the lacunar infarcts and identified the connected cortical area based on a standard brain atlas warped into the subject space. Cortical thickness and microstructural neurite orientation dispersion and density imaging (NODDI) metrics of the ipsilesional and contralesional cortices were compared, and correlations between cortical thickness and NODDI metrics were also investigated. We found decreased cortical thickness and reduced neurite orientation dispersion index (ODI) in the ipsilesional cortex (2.47 vs. 2.50 mm, P=0.008; 0.451 vs. 0.456, P=0.035, respectively). In patients with precentral gyrus involvement (n=23), we found that ODI in the ipsilesional cortex was correlated with cortical thickness (r=0.437, P=0.037), and ODI in the contralesional cortex was also correlated with contralesional cortical thickness (r=0.440, P=0.036). NODDI metrics could reflect cortical microstructural changes following lacunar infarcts. The correlation between decreased ODI and reduced cortical thickness suggests that dendrites' loss might contribute to lacunar infarct-related cortical atrophy.