Silicon (Si) has been regarded as one of the next-generation anode materials due to its ultrahigh theoretical capacity, low equilibrium potential, abundant resources and superior safety performance. Herein, we fabricated a novel honeycomb Si composed of many Si nanoparticles (NPs), which can be refined from the urchin-like crude product obtained through the magnesiothermic reduction process. Via the electrostatic attraction, rapid freeze-drying process and further thermal treatment, the honeycomb Si can be tightly encapsulated in a thin layer composed of reduced graphene oxide and carbon nanotube (indicating as Si-rGO/CNT) to avoid direct exposure to the electrolyte. Si NPs with the wrinkled rGO/CNT wrapping layer containing mesopores can not only shorten the pathway of Li+ ions and electrons but also accommodate the unavoidable expansion/contraction and buffer the excessive stress. Meanwhile, the CNT intertwined throughout the electrode can effectively repair those areas that lost conductivity during long-term cycling. Therefore, the self-supported Si-rGO/CNT electrode having a high Si content of 76 wt% exhibits capacities of 1304 mAh g−1 at 2 A g−1 and 1053 mAh g−1 at 5 A g−1 in rate performance, and maintain a capacities of 1899 mAh g−1 at 0.5 A g−1 after 250 cycles and 1003 mAh g−1 at 4 A g−1 after 1000 cycles accompanying with a stable coulombic efficiency (CE) up to 99.5%.