Mitochondrion is the metabolic center and powerhouse of cells producing cellular energy which plays an important role in various physiological and pathophysiological processes. Recent research demonstrates that mitochondrial energy metabolism mediates the transmission of mitochondrial-nuclear signals through intermediate products which regulates epigenetic presentation of the chromatin and thereby affects gene expression. Epigenetic modification, a genetic regulatory model, is independent of DNA sequence and plays a major role in establishing and maintaining a specific gene's expression profile. Disorders of mitochondrial metabolism can induce epigenetic reprogramming which in turn initiates aging phenotypes and degenerative diseases. This review introduces recent research progress on the relationship between mitochondrial metabolism and chromatin-related epigenetic modification, discusses the role of mitochondrial stress in chromatin recombination, and suggests future research directions and their application in the study of age-related diseases such as cognitive dysfunction.