Coming from a single zygote, monozygotic (MZ) twins share nearly all of their genetic materials and are almost strikingly similar in appearance. Yet they are often discordant for important phenotypes including complex diseases. The study of discordant MZ twins allows us to understand the role of epigenetics in complex traits by controlling many potential confounders, such as genetic factors, maternal effects, age and sex. As we know, DNA methylation is the most stable epigenetic modification. In human, many causal genes, regulating disease status by DNA methylation modification in imprinting disorders, psychological disorders, autoimmune diseases and cancers, have been discovered, which provides a foundation for studying epigenetic regulation of diseases and application of epigenetic drugs. This article reviews the latest findings on DNA methylation status, estimates of DNA methylation heritability as well as studies of DNA methylation regulation in complex traits using MZ twins, in order to provide reference for research on epigenetic modification in complex traits.