The aim of this meta-analysis was to evaluate the accuracy of cardiac magnetic resonance (CMR) in detecting left atrial/left atrial appendage (LA/LAA) thrombus and to analyze the difference between the diagnostic accuracy of various imaging sequences. PubMed, Web of Science, Embase, and the Cochrane Library were systematically searched for studies from 2000 to 2017 that compared CMR with transesophageal echocardiography (TEE) in detecting LA/LAA thrombus. The CMR images were analyzed in four categories: (1)cine-CMR; (2)first-pass contrast-enhanced 3D CMR angiography (CE-MRA); (3)delayed-enhancement CMR (DE-CMR); and (4)CMR, regardless of the magnetic resonance sequences used. Descriptive and quantitative information was extracted and Meta-DiSc1.4 was used to perform the analysis. The analysis included 582 patients from seven publications. The pooled sensitivity, specificity, diagnostic odds ratio, positive likelihood ratio, negative likelihood ratio, and summary receiver operating characteristic of cine-CMR were 91.00%, 93.00%, 50.43, 10.04, 0.24, and 93.93%, respectively; for CE-MRA, the values were 77.00%, 97.00%, 179.21, 51.77, 0.30, and 97.63%, respectively; for DE-CMR, 100.00%, 99.00%, 849.70, 77.62, 0.09, and 99.38%, respectively; and for CMR, 80.00%, 99.00%, 187.54, 24.21, 0.17, and 97.71%, respectively. In patients with atrial fibrillation, CMR has been proven to be afavorable diagnostic technique for the detection and assessment of LA/LAA thrombus. Among the imaging sequences evaluated, DE-CMR had the highest sensitivity, specificity, and diagnostic accuracy.