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Background Atrial fibrillation (AF) patients are prone to stroke and peripheral arterial embolism. Studying the pathogenesis of thrombosis formation in AF and providing effective interventions to reduce the risk is an important direction of clinical and basic research on AF. Objective To investigate the correlation of markers of inflammation and endothelial injury with thrombosis in the left atrium (LA) in AF patients. Methods Twenty-nine patients with valvular heart disease and 10 patients with coronary heart disease who underwent thoracotomy at the First Affiliated Hospital of Guangxi Medical University from July 2017 to December 2019 were selected, and divided into sinus rhythm group (15 cases) and AF group 〔24 cases, including 12 with left atrial appendage thrombus (LAAT), and 12 without LAAT〕 according to heart rhythm. General demographics were collected. Besides that, other data were also collected, including left atrial diameter (LAD) and left ventricular ejection fraction (LVEF), levels of protein kinase B (AKT), nuclear factor-κ B (NF-κ B), high-sensitivity C-reactive protein (hs-CRP), interleukin-6 (IL-6), IL-8, tumor necrosis factor (TNF-α), endothelin-1 (ET-1), nitric oxide (NO), von Willebrand factor (VWF), intercellular adhesion molecule (ICAM-1) and vascular cell adhesion factor (VCAM-1) in the left atrial blood sample, and calculated thrombus area in patients with AF and LAAT. The relationships of LAD, LVEF, markers of inflammation and endothelial injury with calculated area of thrombus in AF with LAAT patients were analyzed by Pearson correlation. Results There were significant differences in LAD and LVEF between sinus rhythm patients and AF patients with or without LAAT (P0.05). AF patients without LAAT had higher levels of AKT, NF-κB, IL-8, ET-1, ICAM-1 and VCAM-1 and lower NO level in left atrium than patients with sinus rhythm (P0.05). The maximum area, minimum area, and average area of the left atrial appendage thrombus in AF patients with LAAT were 4.8 cm2, 1.67 cm2, and (3.48±0.83) cm2, respectively. Pearson correlation analysis showed LAD, LVEF, AKT, NF-κB, hs-CRP, IL-6, IL-8, TNF-α, ET-1, NO, vWF, ICAM-1, and VCAM-1 had no linear correlation with the area of thrombus in AF patients with LAAT (P>0.05) . Conclusion Increased levels of markers of inflammation and endothelial injury in left atrium were found in AF patients, which were even more higher when the patients also had LAAT. Detecting the markers of inflammation and endothelial injury in left atrium is helpful to evaluate the thrombus prevalence in AF patients.