The present study was designed to explore the correlation between serum S100 beta levels and cognitive dysfunction in patients with cerebral small vessel disease (SVD). A total of 172 SVD patients participated in the study, and they were assigned to patients with no cognitive impairment (NCI group) and those with vascular cognitive impairment no dementia (VCIND group). In total, 105 people were recruited into the normal control group. Serum S100 beta protein level was detected by ELISA. A receiver operating characteristic (ROC) curve was employed for the predictive value of serum S100 beta in diagnosing SVD with cognitive dysfunction. Pearson correlation analysis was used to examine the association of S100 beta level with mini-mental state examination (MMSE) and Montreal cognitive assessment (MoCA) and the association of S100 beta levels with hypertension. Logistic regression analysis was used to analyze risk factors of SVD. The serum S100 beta levels in the VCIND group were higher than those in the NCI and normal control groups. Logistic regression analysis revealed that a high serum S100 beta protein level, hypertension, and high low density lipoprotein-cholesterol (LDL-C) level were the independent risk factors for SVD. In addition, hypertension patients showed higher S100 beta levels than those with normal blood pressure and the normal control group, and there was a positive correlation between S100 beta level and blood pressure. The concentration of serum S100 beta level was related to impairment of cognition function of VCIND patients, therefore, early detection of serum S100 beta was of great value for diagnosis of SVD.