Aim To investigate the correlation between flow mediated dilatation (FMD) and the degree of coronary artery lesion and provide a clinical basis for the detection of vascular endothelial function in early coronary heart disease. Methods A total of 130 patients with suspected coronary heart disease (CHD) who underwent coronary angiography (CAG) were recruited. The FMD was performed before CAG. The patients were divided into CHD group and non-CHD group according to the result of CAG. Meanwhile, the differences were analyzed about FMD in different lesion degree of coronary artery. ROC curves were drawn to find the optimal cut-off value for diagnosis of CHD. Results Systolic blood pressure, homocysteine and HbA1c in CHD group were higher than those in non-CHD group (P＜0.01 or P＜0.05). The FMD in CHD group was significantly lower than that in non-CHD group (P＜0.01). Further subgroup analysis showed that the FMD in normal group was higher than that in coronary atherosclerosis group, single branch lesion group, double branch lesion group and three branch lesion group (P＜0.05 or P＜0.01), the FMD in coronary atherosclerosis group was respectively higher than that in double branch lesion group and three branch lesion group (all P＜0.01), the FMD in single branch lesion group was higher than that in three branch lesion group (P＜0.05). Logistic regression analysis indicated that the FMD was an independent predictor of CHD (OR＝0.2,5%CI was 0.068～0.487, P＜0.01). ROC curve analysis showed that FMD≤6.05% was the best cut-off value for predicting CHD, and the sensitivity was 91.1%, the specificity was 80.4%, positive predictive value was 87.8% and the negative predictive value was 85.4%. Conclusion The FMD can better reflect the degree of coronary artery lesions and has a good predictive value for the diagnosis of coronary heart disease.