Rational design of nano-structured silicon (Si)-based composites to enhance the structural stability and electrical conductivity is key to developing high-performance lithium-ion batteries. Here, a supramolecular self-assembly strategy is first adopted to prepare Si@rGO composites with multilayered structure through the modified Hummers method. Experimental results demonstrate that Si@SiOx NPs are uniformly distributed in rGO interlayers by supramolecular interaction. In situ Raman results suggest that the multilayer embedded structure can effectively confine the Si NPs and preserve the integrity of the electrode. Theoretical calculations indicate that the imbalanced charge distribution in inner interface shows enhanced dual-interfacial bonding and charge interactions in the Si@SiOx⊂rGO composite, resulting in an interfacial electric-field between Si NPs and rGO for fast ionic and charge migration. The fabricated MSi@SiOx⊂rGO anode with high Si contents (> 60 wt.% Si) exhibits superior Li-ion reaction kinetics (882.4 mAh g−1 at 8 A g−1), durable structural stability (0.031% per cycle capacity attenuation with an average Coulombic efficiency > 99.7%), and low expansion rate. High-mass-loading electrodes show great potential for commercial applications. Full cells assembled with LiCoO2 cathodes also demonstrate outstanding Li-ion storage properties. This work provides insights into the interfacial design of Si@C anodes for advanced Li-ion battery.