Background Little is known about the association between the cortical microinfarcts (CMIs) and intracranial atherosclerosis (ICAS) in Chinese patients with ischemic stroke. This study was designed to analyze the association and evaluate the role of CMIs in clinical outcomes. Methods We evaluated 1421 consecutive patients who had experienced an acute cerebral ischemia within 7 days after symptom onset and evaluated the presence of CMIs and ICAS based on patients' 3.0-T magnetic resonance imaging and magnetic resonance angiography scans. Baseline characteristics, patient risk factors, and clinical outcomes were analyzed to investigate the different outcomes between the CMIs (n = 209) group and non-CMIs (n = 1212) group. Results CMIs were present in 14.7% persons. The following parameters were associated with risk of CMIs: advanced age, National Institutes of Health Stroke Scale score on admission, lower level of systemic blood pressure, lower triglycerides level, ICAS, and cerebral microbleeds (CMBs). On multivariate logistic regression analysis, ICAS remained an independent risk factor for the development of CMIs (adjusted odds ratio, 1.493; 95% confidence interval, 1.022-2.182; P =.038). At the time point of 1 year after stroke, the rates of poor outcome (modified Rankin Scale, 3-6) in CMIs group (33.5%) were statistically significantly different from the non-CMIs group (22.6%; P =.001). In addition, patients in CMIs group had a significantly higher stroke recurrence rate than patients in the non-CMIs group (6.7% versus 4%; P =.085). Conclusions The development of CMIs is strongly associated with ICAS. CMIs are independent predictors of poor prognosis in patients with ischemic stroke.