Si nanoparticles prepared by ball-milling (BM-Si) are expected as practical negative-electrode materials for lithium-ion batteries, but their performance is much lower than those of more expensive Si nanomaterials, such as chemical-vapor-deposition derived Si nanoparticles (CVD-Si) having a tight network structure. It is found that carbon-coating of aggregations of BM-Si forms a quasi-network structure, thereby making the performance comparable to that of CVD-Si under capacity restriction (to 1500 mAh g−1). In this case, the structural transition of BM-Si during charge/discharge cycling is characterized by the formation of a specific ‘wrinkled structure’, which is very similar to that formed in CVD-Si.