Aim To investigate the relationship between left atrial thrombosis and peripheral blood neutrophil to lymphocyte ratio (NLR) in patients with non-valvular atrial fibrillation (NVAF). Methods 207 NVAF patients diagnosed and treated in our hospital from March 2016 to August 2020 were selected and divided into low NLR group and high NLR group according to the level of peripheral blood NLR. The clinical data of the two groups were compared. The correlation between NLR and clinical indicators and left atrial thrombosis were analyzed. The influencing factors of left atrial thrombosis and their predictive value were analyzed. Results Compared with the low NLR group, the CHADS2 score, CHA2DS2-VASc score, NLR, D-dimer (D-D), serum uric acid (SUA), brain natriuretic peptide (BNP), C-reactive protein (CRP), left atrial dimension (LAD) and ratio of peak mitral early diastolic velocity (E) to peak mitral annular early diastolic velocity (Em) (E/Em) were significantly increased, and left atrial ejection fraction (LAEF) was significantly decreased in the high NLR group (P＜0.05). NLR was significantly positively correlated with CHADS2 score, CHA2DS2-VASc score, D-D, SUA, BNP, CRP, LAD, and E/Em, and significantly negatively correlated with LAEF (P＜0.000 1). CHADS2 score, CHA2DS2-VASc score, NLR, D-D, SUA, BNP, CRP, LAD, and E/Em all had a significant positive correlation with the occurrence of left atrial thrombus (P＝0.000), while LAEF had a significant negative correlation with the occurrence of left atrial thrombus (P＝0.000). CHADS2 score, CHA2DS2-VASc score, NLR, D-D and LAD were the risk factors for left atrial thrombosis (P＜0.05). With the optimal cutoff value of 1.85, the area under the ROC curve of NLR in the prediction of left atrial thrombosis in NVAF was 0.806 (95%CI:0.746～0.865), the sensitivity was 74.82% (95%CI:0.668～0.818), and the specificity was 67.65% (95%CI:0.552～0.785). Conclusion Elevated level of NLR significantly increases the risk of left atrial thrombosis in patients with NVAF. As an independent risk factor for left atrial thrombosis in patients with NVAF, NLR has certain predictive value for left atrial thrombus.