The association between 25-hydroxyvitamin D and cognitive impairment and emotional disorder in patients with cerebral small vessel disease is unknown. This retrospective study included, 504 Chinese patients with cerebral small vessel disease admitted to the Department of Neurology of the First Hospital of Hebei Medical University between June 2019 and October 2021. The Montreal Cognitive Assessment and Hamilton Anxiety Scale (14 items) scores were utilized to divide the patients into four groups. The multivariate Cox regression analysis revealed that low 25-hydroxyvitamin D, high homo-cysteine, hyperuricemia, severity of white matter lesions, and a history of hypertension were independent risk factors for cognitive impairment among patients with cerebral small vessel disease. However, a high level of education is a protective factor. Furthermore, the level of 25-hydroxyvitamin D was significantly associated with the changes in brain functional regions. Serum 25-hydroxyvitamin D is a promising biomarker for predicting cognitive and emotional disorders in patients with cerebral small vessel disease and is highly associated with alterations in brain functional regions.