Objective To analyze the relationship between left atrial appendage (LAA) structure and thrombus formation in patients with non-valvular atrial fibrillation (NVAF). Methods A total of 283 NVAF patients who are undergoing selective radiofrequency ablation in our hospital from January 2012 to January 2021 were enrolled in this study. The medical history and imaging results were collected. The patients were divided into thrombus and non-thrombosis groups based on the results of transesophageal echocardiography. The risk factors of thrombosis were analyzed. SPSS statistics 24.0 was used for statistical analysis. Data comparison between 2 groups was performed using student′s t test, Wilcoxon test or Chi-square test depending on data types. Univariate analysis was used to identify variables with predictive power, followed by multivariate analysis to explore independent risk factors for thrombosis. Receiver operating characteristic (ROC) curve was drawn to evaluate the predictive value of each risk factor for thrombosis. Results There were statistical differences in body mass index, course of atrial fibrillation, CHA2DS2-VASc score, proportion of persistent atrial fibrillation, uric acid and brain natriuretic peptide levels, left ventricular ejection fraction, left atrial diameter (LAD), left atrial appendage volume (LAA-V), left atrial appendage length (LAA-L), left atrial appendage first curvature and left atrial appendage lobes between the thrombus and non-thrombosis groups (P＜0.05). Multivariable logistic regression analysis indicated that CHA2DS2-VASc score (OR=1.898,95%CI 1.223-2.944), LAD (OR=1.214,95%CI 1.087-1.355), LAA-V (OR=1.230,95%CI 1.023-1.480), LAA-L (OR=1.154,95%CI 1.005-1.326), left atrial appendage first curvature (OR=1.032,95%CI 1.003-1.063) and left atrial appendage lobes (OR=2.024,95%CI 1.331-3.077) were independent risk factors for thrombosis. ROC curve analysis showed that CHA2DS2-VASc scores ≥4 (sensitivity 0.575, specificity 0.844), LAD ≥39.5 mm (sensitivity 0.825, specificity 0.716), LAA-V≥7.155 cm³(sensitivity 0.850, specificity 0.724), LAA-L≥25.01mm (sensitivity 0.775, specificity 0.938), LAA first curvature≥121.5°(sensitivity 0.450, specificity 0.951) and LAA lobes ≥3 (sensitivity 0.900, specificity 0.646) significantly increased the risk of LAA thrombosis. Conclusion LAA structure is a good predictor of thrombosis. In anticoagulation decision-making for NVAF patients, clinicians should take the complexity of LAA structure into consideration on the basis of CHA2DS2-VASc score.