Li-ion batteries (LIBs) have demonstrated great promise in electric vehicles and hybrid electric vehicles. However, commercial graphite materials, the current predominant anodes in LIBs, have a low theoretical capacity of only 372 mAh·g⁻¹, which cannot meet the ever-increasing demand of LIBs for high energy density. Nanoscale Si is considered an ideal form of Si for the fabrication of LIB anodes as Si–C composites. Synthesis of nanoscale Si in a facile, cost-effective way, however, still poses a great challenge. In this work, nanoscale Si was prepared by a controlled magnesiothermic reaction using diatomite as the Si source. It was found that the nanoscale Si prepared under optimized conditions (800°C, 10 h) can deliver a high initial specific capacity (3053 mAh·g⁻¹ on discharge, 2519 mAh·g⁻¹ on charge) with a high first coulombic efficiency (82.5%). When using sand-milled diatomite as a precursor, the obtained nanoscale Si exhibited a well-dispersed morphology and had a higher first coulombic efficiency (85.6%). The Si–C (Si : graphite = 1:7 in weight) composite using Si from the sand-milled diatomite demonstrated a high specific capacity (over 700 mAh·g⁻¹ at 100 mA·g⁻¹), good rate capability (587 mAh·g⁻¹ at 500 mA·g⁻¹), and a long cycle life (480 mAh·g⁻¹ after 200 cycles at 500 mA·g⁻¹). This work gives a facile method to synthesize nanoscale Si with both high capacity and high first coulombic efficiency.