Silicon has attracted wide attention due to its high theoretical specific capacity. However, the huge volume change and poor reaction kinetics in the lithiation process lead to a serious deterioration of its structure, a continuous capacity attenuation and a poor magnification performance, thus restricting its practical application. To solve these problems, silicon/reduced graphene oxide (Si/rGO) nanocomposites with a three-dimensional cage-like conductive structure were designed by an in-situ electrostatic self-assembly and hydrothermal reduction method with commercial Si nano-particles with the size of 60 nm and natural flake graphite. The lithium ion storage performance and energy storage mechanism of Si/rGO nanocomposite were investigated. The results show that Si nano-particles are uniformly encapsulated into a three-dimensional cage-like conductive network structure of rGO, effectively limiting the volume expansion of nano-Si particles and providing the more ion transport channels in the process of lithium ion intercalation/detachment. The specific capacity of Si/rGO nanocomposites is 1246 mA·h/g at 0.1 A/g. The Coulomb efficiency is 98.2% and the capacity retention is 95.5% from fifth cycle, indicating that the nanocomposite has a fast stability behavior. The reversible capacity remains 852 mA·h/g, the Coulomb efficiency is 99.9%, and the capacity retention is 68.4% after 200 cycles.