Silicon-based materials are prospective anodes because of the high capability of lithium (Li) storage, but the large volumetric expansion seriously destroys the integrity of the electrodes and further results in unsatisfactory cycling performance. Reasonable structure design based on low-cost nano silicon (Si) prepared by an feasible method is still an enormous challenge. Herein, the carbon-coated and cross-linked carbon nanotube/porous-Si/SiOx microspheres (CNT/SFDP-Si/SiOx@C) are firstly synthesized by combining an inverse water-in-oil microemulsion approach with magnesiothermic reduction. One high value-added route for utilizing silica fume as the precursor to form nano silicon is provided. The collaborative strategy via wired CNTs network, porous-Si/SiOx flexible matrix, and carbon coating is employed to keep the integrity and stability of electrode structure. Benefiting from the synergistic effect of the flexibility of CNTs network, protection of outer carbon shell, doping of diverse nitrogen (N) species, and accommodation of porous-Si/SiOx, CNT/SFDP-Si/SiOx@C exhibits excellent electrochemical performance. The long cycling lifespan with a reversible capacity of 675.8 mAh g−1 after 1000 cycles at 2 A g−1, a slight decay rate per cycle of 0.018 %, and a high-rate performance are simultaneously obtained. The prelithiated LiFePO4||CNT/SFDP-Si/SiOx@C full cell is also assembled, showing the reversible capacity of 129.4 mAh g−1 at 0.2C.