In this work we propose a facile template-sacrificing method to prepare bowl-like silicon@reduced graphene oxide (Si@rGO) hybrids as a high-performance anode for lithium ion batteries (LIBs). Uniform SiO2 spheres were initially synthesized and wrapped by GO, forming a three-dimensional (3D) skeleton. After reduction and etching, Si nanoparticles were obtained and evenly distributed on the flexible rGO layer, resulting in a bowl-like nanoarchitecture. A benefit of this novel structure is that the volume change of Si can be confined during the charge–discharge process. As a result, the Si@rGO anode exhibited a high first discharge capacity of ∼1890 mAh g−1 with a Coulombic efficiency of 90.79% at a current density of 0.1 A g−1. After 100 cycles, a stable specific capacity of 450 mAh g−1 was achieved, which is twice that of pure Si nanospheres (208 mAh g−1) and rGO (260 mAh g−1). Moreover, when the current density increased to 1 A g−1, the specific capacity of Si@rGO was 100 mAh g−1, whereas it was 34 mAh g−1 for Si nanospheres, demonstrating the advantage of Si@rGO. By analyzing the electrochemical behavior, it is found that the outstanding LIB performance of Si@rGO can be ascribed to the involvement of rGO which constructs the 3D nanoarchitecture that acts as a buffer layer to stabilize the Si and promotes Li+ diffusion as well as the conductivity of the electrodes. This work highlights the significance of the microstructure for lithium ion storage performance of Si-based nanocomposites.