Silicon (Si) is known as an advanced anode material in the application of high-energy lithium-ion batteries (LIBs). However, Si-based anodes still face many challenges in practical applications, such as larger volume expansion, poor conductivity, and knotty solid electrolyte interphase films. Enormous efforts are committed to design and develop the Si/C composites with special structures and morphologies in order to overcome the above deficiencies of Si-based anode materials. Herein, the silicon/ silicon oxide/carbon/graphene (Si/SiO x /C/Gr) composite is deliberately designed and synthesized by the magnesiothermic reduction and freeze-drying strategies in which the resorcinol-formaldehyde resin (RF) is used as the carbon source. Moreover, amorphous SiO x and carbon are embedded around the Si nanodomains, which can overcome the bulk change of Si anodes during cycling processes. At the same time, graphene (Gr) can further boost the conductivity of the anode and maintain a stable electrode. Accordingly, the Si/SiO x /C/Gr anode exhibits good cycling performance in LIBs, e.g., a first discharge capacity of 1180 mAh g −1 with an initial Coulombic efficiency of 65.4% and a retention rate of 79.5% after 200 cycles at 0.3 A g −1 , indicating that the Si-based anodes through the rational designing structure and morphology will have good application prospects in high-energy density LIBs.