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In nonvalvular atrial fibrillation (NVAF) patients, the effect of left atrial appendage (LAA) morphology, structure, and hemodynamic characteristics evaluated by real-time 3D transesophageal echocardiography (RT3D-TEE) on thromboembolic risk has not been elucidated.A total of 444 NVAF patients who underwent clinically indicated RT3D-TEE were enrolled in the study. The orifice size, orifice area, depth, and volume measurements of the LAA were assessed using Philips QLAB 9.0. The LAA characteristics were compared among different CHA2DS2-VASc thromboembolic risk subgroups, as well as between the thromboembolic event and nonevent groups.The orifice size, orifice area, and end-diastolic volumes of the LAA were increased with an increasing CHA2DS2-VASc risk score in the NVAF patients, whereas the emptying rate was decreased. The NVAF patients with LAA thrombus exhibited a significantly increased end-diastolic volume (7.39 ± 3.47 versus 5.21 ± 2.59 mL, P = .003) and higher prevalence of the cauliflower shaped LAA (64.3% versus 25%, P = .004) compared with those without thrombus. Logistic regression indicated that the LAA end-diastolic volume (P = .002; odds ratio 1.556; 95% confidence interval 1.176–2.057) and cauliflower shape (P = .001; odds ratio, 10.177; 95% confidence interval, 2.458–42.140) were independent predictors of thromboembolic events in patients with NVAF following adjustment for the CHA2DS2-VASc score.The LAA end-diastolic volume and cauliflower phenotype predict thromboembolic events independent of the CHA2DS2-VASc score, and these data improve stroke prediction in NVAF patients.