Silicon-based materials are the most promising candidates to surpass the capacity limitation of conventional graphite anode for lithium ion batteries. Unfortunately, Si-based materials suffer from poor cycling performance and dimensional instability induced by the large volume changes during cycling. To resolve such problems, nanostructured silicon-based materials with delicately controlled microstructure and interfaces have been intensively investigated. Nevertheless, they still face problems related to their high synthetic cost and their limited electrochemical properties and thermal stability. To overcome these drawbacks, we demonstrate the strategic design and synthesis of a gyroid three-dimensional network in a Si@SiOx/C nanoarchitecture (3D-Si@SiOx/C) with synergetic interaction between the computational prediction and the synthetic optimization. This 3D-Si@SiOx/C exhibits not only excellent electrochemical performance due to its structural stability and superior ion/electron transport but also enhanced thermal stability due to the presence of carbon, which was formed by a cost-effective one-pot synthetic route. We believe that our rationally designed 3D-Si@SiOx/C will lead to the development of anode materials for the next-generation lithium ion batteries.