N6-methyladenine (6mA) is an epigenetic modification existed in eukaryotes, which dynamically regulates transcription by modifying mitochondrial DNA, non-coding genes and ribosomal DNA. Current studies have found that 6mA affects mitochondrial activity and function by regulating mitochondrial DNA transcription, etc., and then participates in the occurrence and development of metabolic diseases. This paper discusses the mechanism of 6mA regulating mitochondrial function and its role in metabolic diseases such as obesity, atherosclerosis, hypertension and cancer, which is expected to provide new ideas for the prevention and treatment of metabolic-related diseases.