We synthesized nanocomposite anodes for lithium-ion batteries consisting of carbon enwrapped Si/SiOx core-shell nanoparticles in order to address the poor cycling performance of silicon and the low initial coulombic efficiency related to SiOx-based materials. In particular, we used varying carbon coating times to examine the effects of carbon growth on the amorphous SiOx layer that critically determines the nanocomposites’ electrochemical properties. Through careful microstructure analysis, three steps for carbon growth on SiOx are suggested. Furthermore, the effects of this stepwise carbon growth on the electrochemical properties of the nanocomposites are investigated. Finally, the optimum carbon coating condition for best electrochemical performance of the nanocomposites is proposed. The nanocomposite with optimal carbon layer thickness provides a high capacity (2167mAhg−1 at 0.5Ag−1) with a notably improved initial coulombic efficiency (76%), excellent cycling performance (84% capacity retention up to 50 cycles) and significantly reduced swelling. The novel nanocomposite synthesis is simple and cost-effective, and as a result a promising approach for future mass production of high-performance composite anode.