Left atrial appendage (LAA), a blind pouch, accounts for more than 90% of the source of cardiac thrombus formation. Contrast retention (CR) in the LAA has been frequently observed during left atrial appendage occlusion (LAAO) procedures, especially in patients with stroke history. This study was designed to assess the relations between LAA contrast retention and thrombogenesis risk of the LAA in patients with non-valvular atrial fibrillation. A total of 132 consecutive patients who underwent LAAO were enrolled. The data collected from computed tomography (CT), transthoracic echocardiography (TTE), transesophageal echocardiography (TEE) and blood samples were analyzed. Univariate and multivariate logistic regression models were constructed to assess the association between CR, left atrial appendage thrombus (LAAT) and other factors. Contrast retention was observed in 33 patients, accounting for 25% of the population. Compared to the non-CR group, patients in the CR group had a larger left atrium anteroposterior diameter (49.64 ± 11.57 vs. 42.42 ± 7.04, P = 0.002), higher CHADS (3.88 ± 0.99 vs. 2.97 ± 1.35, P = 0.001) and CHADS-VASc scores (5.79 ± 1.14 vs. 4.89 ± 1.56, P = 0.003), a higher rate of prior stroke (90.9% vs. 66.7%, P = 0.007), more LAA lobes (3.13 ± 1.18 vs. 2.64 ± 1.12, P = 0.038), and a higher prevalence of LAAT (63.6% vs. 13.1%, P < 0.001). After having adjusted the logistic model, only contrast retention, LAA cauliflower morphology and left ventricular ejection fraction (LVEF) were independently associated with LAAT. Patients with LAA contrast retention have a higher risk of left atrial appendage thrombosis. Contrast retention may be a cardiac factor strongly associated with cardiogenic stroke.