Nano-silicon has been regarded as the most promising anode material for next-generation lithium-ion batteries (LIBs). However, the preparation of nano-silicon suffers from high cost, complex procedures, and low yield, which hinders its commercial application. In this study, porous nano-silicon with particle sizes in the range of 50–100 nm was prepared through molten salt-assisted magnesiothermic reduction using porous nano-silica derived from clay minerals as the precursor. Through combining ball milling and acid activation, the synthesised nano-silica derived from montmorillonite exhibited smaller particle sizes (below 50 nm), higher specific surface area (647 m2 g–1), and total pore volume (0.71 cm3 g–1). This unique structure greatly facilitated the conversion efficiency of silica into nano-silicon by maximising the contact area between silica and magnesium powder and optimising the diffusion kinetics of magnesium atoms. When used as anodes in LIBs, the synthesised nano-silicon materials demonstrated a high specific capacity of up to 1222 mAh g–1 and an excellent capacity retention rate of 79% after 150 cycles at a current density of 0.5 A g–1. This method provides a novel approach for the cost-effective and large-scale production of nano-silicon materials for high-performance anodes.