Spermatogenesis is a highly complex and unique differentiation process. This process involves development of spermatogonia into spermatocytes, formation of haploid spermatids, and maturation of spermatozoa. It features stage- and testis-specific gene expression, mitotic and meiotic divisions, and the histone-protamine transition. The epigenetic modification plays an important role in meiotic recombination, formation of the synaptonemal complex, sister chromatid cohesion, spermiogenesis during postmeiotic stages, gene expression repression, and heterochromatin formation. The mark of the repressive and/or activating histone methylation and acetylation has a defined composition. It not only ensures proper chromosome pairing and successful bivalent segregation but also mediates highly orchestrated expression of meiosis-specific genes. The incorrect histone methylation and/or acetylation during spermatogenesis will directly affect the establishment and maintenance of epigenetic patterns, resulting in abnormal spermatogenic cells and even male infertility. This article is an effort to review the dynamic changes of methylation and acetylation of histones during spermatogenesis, as well as the regulatory mechanism of the enzymes involved in these processes, which provides some basic information for further study of the epigenetic events during spermatogenesis and the prevention of male infertility.