Epigenetics refers to heritable changes in gene expression without alteration of the DNA sequence. Epigenetic changes play an important role in a variety of biological processes including glucose and lipid metabolism. Glucose and lipid metabolism is closely related each other in vivo and abnormal lipid and glucose metabolism is able to cause multiple metabolic related diseases. This review focuses on recent advances of DNA methylation, histone modification, and non-coding RNA on regulating glucose and lipid metabolism.