Abstract The superstructure composed of various functional building units is promising nanostructure for lithium‐ion batteries (LIBs) anodes with extreme volume change and structure instability, such as silicon‐based materials. Here, a top‐down route to fabricate Si/SiO 2 @graphene superstructure is demonstrated through reducing silicalite‐1 with magnesium reduction and depositing carbon layers. The successful formation of superstructure lies on the strong 3D network formed by the bridged‐SiO 2 matrix coated around silicon nanoparticles. Furthermore, the mesoporous Si/SiO 2 with amorphous bridged SiO 2 facilitates the deposition of graphene layers, resulting in excellent structural stability and high ion/electron transport rate. The optimized Si/SiO 2 @graphene superstructure anode delivers an outstanding cycling life for ≈1180 mAh g −1 at 2 A g −1 over 500 cycles, excellent rate capability for ≈908 mAh g −1 at 12 A g −1 , great areal capacity for ≈7 mAh cm −2 at 0.5 mA cm −2 , and extraordinary mechanical stability. A full cell test using LiFePO 4 as the cathode manifests a high capacity of 134 mAh g −1 after 290 loops. More notably, a series of technologies disclose that the Si/SiO 2 @graphene superstructure electrode can effectively maintain the film between electrode and electrolyte in LIBs. This design of Si/SiO 2 @graphene superstructure elucidates a promising potential for commercial application in high‐performance LIBs.