Electromagnetic waves at terahertz (THz) frequencies have been shown to have diverse effects on the properties of cytoplasmic membranes. Mitochondria, which are double-membrane organelles within cells and served as the center of energy metabolism, are critical in neuronal growth. However, the specific impacts of terahertz waves on mitochondrial membranes have not been conclusively confirmed. Several studies have indicated that THz radiation can alter phospholipid membrane structures, subsequently leading to functional changes in cells. Given that the composition of the mitochondrial membrane is similar to that of the cell membrane, it has been hypothesized that THz waves could also affect mitochondrial membranes, thereby influencing mitochondrial function. To explore this, liposomes and molecular models of mitochondrial membrane structures were constructed, revealing that the disturbances in membrane structure were akin to the process of electroporation. These findings suggest that THz electromagnetic waves could potentially be used as a tool for regulating mitochondrial and other membrane structures in vitro.