Graves disease (GD), also known as toxic diffuse goiter, is the most common cause of hyperthyroidism. Recent studies have shown that the interaction between genetic susceptibility and environmental predisposing factors is possibly the key cause of GD, and epigenetics is a bridge between the environment and genetics. Evidence indicates that epigenetic changes including DNA methylation, histone covalent modification, and gene silencing mediated by non-coding RNA molecules play an important role in the pathogenesis of GD. This article mainly describes the epigenetics involved in the pathogenesis of GD and its potential clinical applications.