Three-dimensional (3D) conductive skeletons can optimize electron/Li-ion migration kinetics and alleviate stress accumulation for silicon (Si)-based electrodes. In this study, the modified carbon nanotubes (MCNs) are used as a stress-buffering and high-speed conducting framework, and a hierarchical structure of 3D MCNs interspersed with flour-derived 2D N-doped C layer is designed for Si anode via molecular self-assembly and in-situ carbonization strategies. Experimental and theoretical calculations show that the charge redistribution occurred in the fabricated SiOx and N-doped C interfaces, which induced an electric field response and increased the interfacial electron/Li-ion transfer rate. Multiphysics simulations show that the 2D/3D hierarchical structures of carbon can optimize the physicochemical properties, such as a favorable local electronic environment, flexible stress dissipation mechanisms and good thermal stability. The prepared electrode with 77.1 wt% Si@SiOx shows a low volume expansion rate of 23 % and has an excellent Li-ion storage capability (972.1 mAh g−1 at 4000 mA g−1). Moreover, the structural stability of fabricated Si-based electrodes is enhanced, achieving 0.04 % per cycle capacity decay for 500 cycles at 2000 mA g−1. Such integrating the 2D/3D carbon framework to manipulate Si interfacial properties provides fundamental research for other electrodes plagued by significant volume expansion.