Magnesiothermic reduction (MR) is an exothermic chemical reaction that can readily convert SiO 2 @C to a Si@C yolk structure, which is of particular interest for high-energy-density lithium-ion batteries (LIBs). However, during MR, crystallinity change from amorphous to graphitic carbon has rarely been reported. Herein, we report partial graphitization along with pore blockage of amorphous carbon (C) of SiO 2 @C during MR, resulting in Si within the partially graphitized carbon (Si@gC) yolk−shell structure. The exothermic heat generated during the MR affects the crystallinity of C to gC, leading to pore blockage. When hollow C (HC) and hollow gC (HgC) are used for LIBs, HgC exhibits superior rate retention and initial Coulombic efficiency (ICE) than HC owing to higher electrical conductivity and lower surface area. Therefore, when Si@gC is used for LIBs, it shows outstanding ICE and rate performance with excellent long-term stability over 300 cycles at 2 C, clearly demonstrating the beneficial effect of graphitization.