Objective To systematically review the relationship between subclinical thyroid dysfunction and the risk of atrial fibrillation.Methods Databases including PubMed, EMbase, The Cochrane Library, Web of Science, CNKI, CBM, VIP and WanFang Data were electronically searched to collect cohort studies on associations between subclinical thyroid dysfunction and atrial fibrillation from inception to June 2020. Two reviewers independently screened literature, extracted data, and evaluated risk of bias of included studies. Meta-analysis was then performed using RevMan 5.3 software.Results A total of 11 studies involving 620 874 subjects and 19 781 cases were included. Meta-analysis showed that subclinical hypothyroidism was not associated with atrial fibrillation (adjusted RR=1.20, 95%CI 0.92 to 1.57, P=0.18) and subclinical hyperthyroidism could increase the risk of atrial fibrillation (adjusted RR=1.65, 95%CI 1.12 to 2.43, P=0.01). subgroup meta-analysis showed that: for the community population, subclinical hypothyroidism was not associated with atrial fibrillation (adjusted RR=1.03, 95%CI 0.84 to 1.26, P=0.81); for the cardiac surgery, subclinical hypothyroidism could increase the risk of atrial fibrillation (adjusted RR=2.80, 95%CI 1.51 to 5.19, P=0.001); subclinical hyperthyroidism could increase the risk of atrial fibrillation among patients with TSH≤0.1 mlU/L (adjusted RR=2.06, 95%CI 1.07 to 3.99, P=0.03) and TSH=0.1～0.44 mlU/L (adjusted RR=1.29, 95%CI 1.01 to 1.64, P=0.04). Conclusions Subclinical hypothyroidism is not associated with atrial fibrillation and subclinical hyperthyroidism can increase the risk of atrial fibrillation. Due to limited quantity and quality of included studies, more high quality studies are required to verify above conclusions.