Arrhythmia is an early abnormal manifestation of the heart. Atrial fibrillation is the most common arrhythmia in the clinic. However, its pathophysiological mechanism has not been fully elucidated. The risk of arrhythmias in drug therapy and the high cost of catheter ablation are clinical challenges. In recent years, metabonomics has made great progress in revealing the biomarkers and pharmacological effects of atrial fibrillation. This article reviews the pathogenesis, metabonomics research method , and biomarkers of atrial fibrillation to expand research ideas to prevent and treat atrial fibrillation.