Mitochondrial ultrastructure is a fine structure observed by electron microscope, which can be changed according to different energy requirements and physiological environment, and plays a key role in regulating mitochondrial function. The structure of mitochondrial cristae is an important mitochondrial ultrastructure, which affects many mitochondrial diseases. Therefore, studying the function and understanding the regulation mechanism of mitochondrial ultrastructure have important guiding significance for studying mitochondrial diseases and looking for therapeutic targets. This paper introduces the main regulating mechanism of mitochondrial cristae in detail, and focuses on the research progress in the composition of mitochondrial ultrastructure, the effect of mitochondrial ultrastructure on mitochondrial function, and the relationship between mitochondrial ultrastructure and mitochondrial disease, in order to provide theoretical reference for developing more effective mitochondrial disease treatment.