In this study, we designed degraders for mitoTPD technology, comprised of a mitochondrial protease activator linked to a ligand for the POI. By applying this conceptual framework, we successfully induced the degradation of mSA localized within mitochondria. Furthermore, by targeting STMP1, which is involved in mitochondrial fission, we demonstrated the feasibility of chemical control of mitochondrial morphology. Given the involvement of mitochondria and mitochondrial proteins in diseases such as cancer and neurodegenerative disorders, the TPD technology developed in this study has the potential to open up new options for drug discovery targeting mitochondria. Notably, our mitochondrial mSA degrader 1 exhibited degradation activity within 2-4 hours. Additionally, the degrader's potency could be adjusted by changing the linker length.