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Cerebral small vessel disease (CSVD) is the most common cause of vascular cognitive impairment (CI). However, the cognitive performance of individuals with CSVD varies considerably. Early identification of neuroimaging changes related to CI caused by CSVD is important for the prediction and management of CI. The present study aimed to explore the early alterations in cortical thickness and regional homogeneity (ReHo) related to CI in people with CSVD. A total of 106 participants with CSVD with CI, 77 participants with CSVD without CI, and 121 control participants underwent neuropsychological tests and multimodal magnetic resonance imaging scans. Cortical thickness was analyzed using FreeSurfer software, and ReHo patterns were explored using the DPARSF toolbox in brain regions that exhibited alterations in cortical thickness. The CSVD with CI group exhibited decreased cortical thickness but normal ReHo in the right anterior cingulate gyrus (ACG), right cuneus, bilateral insula, and right middle temporal gyrus compared with that in the other two groups. Specifically, both cortical thickness and ReHo in the right ACG were significantly associated with memory performance in CSVD patients with CI. In addition, impaired visuospatial function occurred earlier than the decline of global function in CSVD patients and was related to cortical thinning in the right middle temporal gyrus. In conclusion, decreased cortical thickness but normal ReHo in the right ACG, right cuneus, bilateral insula, and right middle temporal gyrus are characteristic alterations related to the development of CI in CSVD patients. These findings may contribute to the early prediction of CI in CSVD patients.