Mesoporous silica nanoparticles (MSNs) have gained wide application as excellent carrier materials; however, their limited degradation in the biological system and potential chronic toxicity pose challenges to their clinical applications. Previous studies have focused on optimizing the elimination performance of MSNs; interestingly, silicon has been well-documented as an essential body component. Therefore, converting MSNs into a form readily utilizable by the organism is a way to turn waste into a valuable resource. However, the recycling and utilization of MSNs are associated with significant hurdles. This study proposes an approach to impede the formation of siloxane, the crucial core in MSNs, by introducing a gradient concentration of Mg. The invasion of Mg significantly reduces the stability of Si-O-Si bonds by substituting silicon ions while preserving the functional three-dimensional structure. Recycling the increased release of Mg and Si ions enhances cellular antioxidant capacity, reduces oxidative stress reactions, improves mitochondrial function, and regulates macrophage inflammatory states. The proposed approach to converting MSN materials shows significant advantages for tissue regeneration in the periodontal defect model. This study opens an insight for applying MSNs in clinical applications in regenerative medicine.