We established a self-decomposable SiO₂ encapsulated mitochondrial targeting short peptide SS31 drug loading system (SiO₂@SS31) to determine its nano-sustained release characteristics in eukaryotic cells. We explored the protection of SiO₂@SS31 on the 661W cells after oxidative injury by H₂O₂. After the drug loading, we detected the morphology of SiO₂@SS31 by transmission electron microscopy (TEM). Moreover, high-pressure liquid chromatography (HPLC) was used to determine the drug capacity and encapsulation efficiency of the nanoparticles. Then, the release curve in vitro was drawn. The 661W cells were cultured in vitro to allow the detection of cytotoxicity by the MTT assay. The SS31loaded nanoscale microspheres labeled with fluorescein isothiocyanate (SiO₂@FITC-SS31) were prepared, and their sustained release effect was detected with intracellular endocytosis, using confocal microscopy and flow cytometry. Within 15 days, the SiO2@SS31 nanoparticles were completely decomposed and simultaneously released the SS31 peptide in deionized water and normal saline. Nonetheless, the process was faster in simulated body fluid and serum. The MTT assay suggested that SiO₂@SS31 has sustained protection compared with SS31 in the 661W cells at 48 h. Flow cytometry proved SiO₂@FITC-SS31 could maintain a high level and last longer after 24 h. The SS31 peptide, which has excellent medical application prospects, can be slowly and continuously released from self-decomposable SiO₂ and targeted to concentrate on mitochondria.