Heterosis is a complex biological phenomenon and has been widely used in agricultural production. However, the formation mechanisms and molecular basis for of this phenomenon remains elusive. The further development of epigenetics, especially the development of techniques in DNA methylation, small RNA and histone modification, provides new strategy and approaches for the study of the molecular bases of heterosis. The previous researches indicate that there was a certain relationship between the varied level of DNA methylation, small RNA, histone and heterosis in hybrid. DNA methylation, small RNA and histone modification played important roles in heterosis. Meanwhile, the interaction amongof DNA methylation, small RNA and histone modification involved in gene expression which lead to the formation of heterosis. This paper review summarizeds the progress of the role and genetic mechanism of epigenetics in heterosis in recent years, as well as the problems and key issues which should be focused in the following researches. It will be helpful for the better understanding of the mechanism of heterosis, and facilitate the study on the epigenetic basis of heterosis and application in plant breeding in the future.