A novel method was developed to synthesize ordered sandwich-structured magnesiothermo-reduced Si nanoparticles (MR-Si NPs)-thermally reduced graphene oxide (TRGO) nanocomposites that combines magnesiothermic reduction, freeze-drying, and thermal reduction. The MR-Si NPs were dispersed into ordered graphene oxide (GO) layers with the aid of sonication. This MR-Si@TRGO composite structure was retained by freeze-drying and followed by thermal reduction. The key features of the nanocomposites, including nanoparticle crystal phase, size, and dispersity on the TRGO matrix, could be controlled by tuning reaction conditions such as reduction temperature and duration. The influence of the weight ratio of active materials: conductive agent: binder, the types of binder, and the content of electrolytes on the electrochemical performance as an anode in lithium-ion batteries was systematically investigated. The electrode fabricated using the MR-Si@TRGO nanocomposites under optimized conditions (80:10:10 for the weight ratio of MR-Si@TRGO: acetylene black: CMC; the electrolyte containing 5 v% vinylene carbonate) exhibited a reversible capacity of 746mAhg−1 after 160 cycles at 1000mAg−1, which is substantially higher than 701mAhg−1 after 120 cycles for the MR-Si@TRGO in the absence of vinylene carbonate, 330mAh g−1 for commercial graphite reported, and 10mAhg−1 for pure MR-Si NPs tested at 200mAg−1 with a weight ratio of 50:30:20 optimized for active materials: acetylene black: PVDF.