Male infertility is one of the major diseases that affect human health and social life, and is influenced by many genetic and environmental factors. Epigenetic modification on DNA strands in response to environmental factors plays an important role in the process of spermatogenesis. Abnormalities of epigenetic regulation may affect both the quantity and quality of sperm production and result in disorders of male reproduction. We hereby review recent progress made in research on epigenetic regulation including DNA methylation, histone modification and non-coding RNA related with male infertility.