The application of high-performance silicon-based anodes, which are among the most prominent anode materials, is hampered by their poor conductivity and large volume expansion. Coupling of silicon-based anodes with carbonaceous materials is a promising approach to address these issues. However, the distribution of carbon in reported hybrids is normally inhomogeneous and above the nanoscale, which leads to decay of coulombic efficiency during deep galvanostatic cycling. Herein, we report a porous silicon-based nanocomposite anode derived from phenylene-bridged mesoporous organosilicas (PBMOs) through a facile sol–gel method and subsequent pyrolysis. PBMOs show molecularly organic–inorganic hybrid character, and the resulting hybrid anode can inherit this unique structure, with carbon distributed homogeneously in the Si-O-Si framework at the atomic scale. This uniformly dispersed carbon network divides the silicon oxide matrix into numerous sub-nanodomains with outstanding structural integrity and cycling stability.