Objective Cerebral microbleeds (CMBs) are one of main manifestations of cerebral small vessel diseases. However, the association between cerebral atherosclerosis and CMBs remains unclear. The aim of this study is to investigate their relationships. Methods Consecutive patients with first-ever ischemic stroke admitted in the Nanshan Hospital from January 2013 to October 2014 were recruited in this study. They were divided into CMBs group (n＝63) and non-CMBs group (n＝67) according to the results of susceptibility-weighted imaging (SWI). Based on the locations of arterial stenotic lesions, they also were assigned into intracranial vessel group, extracranial vessel group and combined group. The presences and extents of the involved vessels and steno-occlusion were used to evaluate the cerebral atherosclerotic burden. The demographic data, biochemical variables, vascular risk factors and numbers of CMBs were collected, compared and analyzed. Results A total of 130 subjects were enrolled. Ordinal logistic regression analysis showed that the extent of atherosclerotic burden was positively correlated with the numbers of CMB (the numbers of arterial lesions, OR＝1.22, 95%CI 1.05?1.42, P＝0.012; the extents of steno-occlusion, OR＝1.25, 95%CI 1.12?1.40, P＜0.001). Especially, the intracranial atherosclerosis was more significantly positively correlated with the numbers of CMBs (the number of arterial lesions, r＝0.51, P＝0.004; the extents of steno-occlusion, r＝0.62, P＜0.001). Conclusion CMBs are closely associated with cerebral atherosclerosis, and the association may be closer between the intracranial atherosclerosis with CMBs.