Epigenetics is the important component of functional genomics. It can be defined as the study of the interplay between environment and genetics, and the study of the heritable change that is not strictly dependent on DNA sequence. Nasopharyngeal carcinoma (NPC) is the common malignant tumor in south China. As a polygenetic inheritance tumor, NPC has the characteristic of obvious tendency of familial aggregation, possesses genomic instability, and is vulnerable to physical, chemical and biological carcinogenic factors. This specific etiological system of NPC refers that it is one of the best model for studying cancer epigenetics. The main point of this review focuses on the progress of studying on the effects of DNA methylation, histone modification, chromatin remodeling and non-coding RNA regulation on the pathologenesis of NPC, and suggests future directions to thoroughly explore the epigenetic pathologenesis of NPC. Moreover, it will open a new prerequisite foundation for finding the epigenetic molecular marks for screening the high-risk susceptibility population, early diagnosis, treatment and prognostic indentification of NPC.