We did this study to find out the clinical manifestations and prognosis of left atrial thrombosis in different types of atrial fibrillation and the relationship with systemic thromboembolism, hoping to find a better therapy strategy. A single-center retrospective study enrolled patients with definite diagnosis of atrial fibrillation complicated with left atrial thrombosis. Data of general clinical information, anticoagulation medications, thromboembolism events, and thrombosis prognosis were recorded and analyzed. A total of 103 patients were enrolled. Compared with non-valvular atrial fibrillation (NVAF), thrombosis outside the left atrial appendage (LAA) was much more common in valvular atrial fibrillation (VAF) with p=0.003. Total prevalence of systemic thromboembolism was 33.0%. Thrombi disappeared in 78 cases (75.7%) under anticoagulation treatment within 2 years. There was no significant difference between warfarin, dabigatran, and rivaroxaban on thromboembolism events and thrombosis prognosis in NVAF, with p=0.740 and 0.493, respectively. Atrial fibrillation patients with LA thrombosis have a high risk of systemic thromboembolism events. Compared with NVAF, patients with VAF had higher incidence of thrombosis outside the LAA. Standard stroke-preventing doses of anticoagulants might not be sufficient to deplete all LA thrombi. There was no statistically difference between warfarin, dabigatran, and rivaroxaban for depleting LA thrombi in NVAF patients.© The Author(s), under exclusive licence to Springer Nature Switzerland AG 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.