Mitochondria is a kind of semi-autonomous organelle, which integrates three basic life activities: material metabolism, energy metabolism and genetic variation, and its metabolism is at the core of cell metabolic network. Current metabonomics mostly focuses on the metabolic characteristics of the whole cell, but lacks the specific reflection of mitochondrial metabolism. Therefore, it is necessary to study the metabolism of mitochondria. Traditional Chinese medicine has unique advantages and characteristics in treating diseases based on syndrome differentiation. Mitochondrial metabolism is also one of its important targets. The study of traditional Chinese medicine based on mitochondrial metabonomics is helpful to reveal the mechanism and target of traditional Chinese medicine in energy metabolism network from the perspective of mitochondrial metabolism. At present, there are many problems and difficulties in mitochondrial metabonomics research, such as the extraction, separation and evaluation of mitochondria, metabolites and so on. This paper summarizes the present situation of mitochondrial metabonomics and its research progress in the field of traditional Chinese medicine, which provides technical support and new research direction for the scientific research of traditional Chinese medicine.