This study aims to realize controllable synthesis of Si-based nanostructures from common and easily accessible silica nanoparticles and to study their component/structure-dependent electrochemical performance as an anode of lithium-ion batteries (LIBs). To this end, a controllable route based on deliberate design has been developed to prepare hollow Si-based nanospheres with tunable composition and crystal structure at the nanoscale. The synthesis process started with coating silica nanoparticles with a carbonaceous polymer with a controllable thickness followed by magnesiothermic reduction. An Si-SiC-C composite was finally produced with a unique hollow sphere structure featuring Si-SiC nanoparticles encapsulated by a cross-linked carbon film network. In addition to the scalability of the synthetic route, the resulting composite exhibits a number of advantageous properties, including excellent electrical conductivity, highly accessible surfaces, structural coherence, and a favorable structure for the formation of a stable solid-electrolyte interphase, which makes it attractive and promising for advanced anode materials of LIBs.