Nanostructured silicon (Si) is a promising candidate for use in lithium ion batteries. In this work, one-dimensional SiO2 was obtained using linear polyethyleneimine (LPEI) as a biomimetic template/scaffold/catalyst, which was subsequently employed to fabricate nanostructured Si with a size of less than 10nm in a SiO2 matrix using a solid–solid magnesiothermic reaction at a relatively low temperature of 500°C. This procedure proved to be cost-effective and high-yielding and generated a product that could withstand a significant Si volume change during lithium insertion/extraction by combining the advantages of Si nanostructures with the buffer effect of the SiO2 matrix. In this manner, excellent cycling stability and a discharge capacity of more than 900mAh/g were observed after 50 cycles. This work expands the structure-derived applications of bioinspired/biomimetic silica.