Display omitted •Effects of dislocation and SF on the performance of Si anode were revealed.•Si anode can be used for the storage of Na and Mg with the 30° partial dislocation.•Na and Mg may concentrate in the 30° partial dislocation core and SF region.•30° partial dislocation and SF may limit the charge/discharge rate of NIBs and MIBs. While the perfect Si can’t be used to store Na and Mg interstitials in Na-ion batteries (NIBs) and Mg-ion batteries (MIBs), the defects of 30° partial dislocation and stacking fault (SF) may improve the performance of Si anode according to the multi-scale simulation results. It is found that both 30° partial dislocation and SF can provide more stable sites to accommodate impurities and enhance the binding strengths. The 30° partial dislocation can drastically promote the binding energies of Na (Mg) to the value of 0.72 (0.622)eV and 0.684 (0.6)eV at Oct-A and Oct-B, respectively. Moreover, it is thermodynamically and kinetically favorable for Na and Mg concentrating in the defect areas. On the other side, the migration barriers of Na and Mg in the 30° partial dislocation and SF are much higher than the defect-free Si. Those defects may restrict the diffusion of interstitials and turn into limiting factors of charge/discharge rate of NIBs and MIBs.