One of the greatest challenges in developing SiO2/C composites as anode materials in lithium ion batteries (LIBs) is to improve the ability of Li storage at high rate over long-term cycles. Herein, biomass rice husks-based hierarchically porous SiO2/N-doped carbon composites (BM-RH-SiO2/NC) were prepared by ball mill and thermal treatment. BM-RH-SiO2/NC can still retain a reversible capacity of 556 mAh g−1 over 1000 cycles at a high current of 1.0 A g−1. At 5.0 A g−1 the capacity is kept as high as 402 mAh g−1. This impressively long-term cyclic performance and high-rate capability of BM-RH-SiO2/NC can be ascribed to the synergetic effect between the natural SiO2 nanoparticles (< 50 nm) and the NC layer. The coating NC layer can not only effectively mitigate the volume strain during charge-discharge process to offer stably cyclic performance but also improve the electrical conductivity. Furthermore, the hierarchical porosity and better electrolyte wettability offer the rapid Li+ diffusion and electron transfer, which enhance the pseudocapacitive behavior of whole electrode material and then guarantee fast electrochemical kinetics. Importantly, the unique Li-storage mechanism of active SiO2 in BM-RH-SiO2/NC composite was formed and found, which further validates the improved electrochemical capability.