Mitochondria are the main organelle for the tricarboxylic acid cycle to produce adenosine triphosphate (ATP), which provides energy for life activities. Mitophagy is a protective Mechanism by which cells selectively remove damaged and redundant mitochondria through autophagy to maintain the stability of mitochondrial quality and quantity. Many researches have confirmed that insulin resistance and insufficient insulin secretion caused by mitochondrial dysfunction are closely related to the occurrence and development of type 2 diabetes mellitus(T2DM). Yin deficiency and dry heat is the central pathogenesis of diabetes, and nourishing Yin and clearing heat are the main treatment. The biological essence of the treatment is a key step to objectively understand the microscopic syndrome differentiation and treatment of T2DM in traditional Chinese medicine. In this article, the relationship between mitochondrial autophagy and T2DM was summarized, and the relationship between mitophagy and treatment of relieving T2DM and nourishing Yin and clearing heat was reviewed.