Co-doping in Si nanocrystals (Si NCs) is an intriguing research topic as the co-doping mechanism at the nanoscale is considerably more complex than the bulk Si. In this study, we utilized ab initio molecular dynamics simulations to investigate the impact of phosphorus (P) and boron (B) co-doping on the properties of Si NCs in the SiO 2 matrix. Our findings demonstrate that P and B impurities exhibit a tendency to aggregate within sub-interfaces and interfacial regions. Furthermore, introducing B impurities during the co-doping process facilitates bonding between P and B near the interface to form P−B pairs. The results of ionic conductivity derived from the diffusion coefficient indicate that with increasing B concentration, the conductance activation energy first decreases before increasing, implying that the introduction of B impurity leads to greater bonding of P impurity to Si or B atoms. Vibrational simulations and bonding configurations on the structure reveal that P−B pair formation weakens the intensity of the vibrational density peak due to the P−B co-doping process, thereby stabilizing the structure.