To investigate the correlation between carotid artery stenosis (CAS) measured by magnetic resonance imaging (MRI) and the coronary stenosis (CS) determined by computed tomography angiography (CTA). In this prospective study, 42 subjects diagnosed with coronary artery disease (CAD) underwent MRI and CTA examinations. The severity degree and number of CAS, the score, detection rate and type of carotid plaque, and also the severity degree and number of CS were assessed. Spearman's rank correlation test was used to evaluate the correlation between CAS and CS. CS was detected in 42 (100%) subjects, while CAS was detected in 36 (85.7%) subjects. Distribution of CAS severity grades in multiple-vessel group was significantly different from other groups, which with more moderate and severe stenosis (p < 0.05). A positive and significant correlation between the CAS severity and CS severity (r = 0.612, p < 0.05), and the number of involved coronary vessels (r = 0.572, p < 0.05) were observed, respectively. Both detection rate (r = 0.587, p < 0.05) and score (r = 0.735, p < 0.05) of carotid plaque showed a good correlation with the number of involved coronary vessels. After carotid MRI, 71 carotid plaques were detected in 42 subjects, with an incidence rate of 9.9% in subjects with mild CS, 18.3% in moderate CS and 71.8% in severe CS. Correlation between CAS measured by MRI and CS determined by CTA was identified in present study. These results indicated that the non-invasive CAS evaluation employing the MRI may be clinically useful for the assessment of CS.