Recently, Si/C composite materials have attracted enormous research interest as the most promising candidates for the anodes of next-generation lithium-ion batteries, owing to their high energy density and mechanical buffering property. However, the fundamental mechanism of Li diffusion behavior in various Si/C composite materials remains unclear, with our understanding limited by experimental techniques and continuum modeling methodologies. Herein, the atomic behavior of Li diffusion in the Si/C composite material is studied within the framework of density functional theory. Two representative structural mixing formats, that is, simple mixture mode and core–shell mode, are modeled and compared. We discover that the carbon material increases Li diffusion in silicon from 7.75 × 10–5 to 2.097 × 10–4 cm2/s. The boost is about 50% more obvious in the mixture mode, while the core–shell structure shows more dependence on the atomic structures of the carbon layer. These results offer new insights into Li diffusion behavior in Si/C composites and unlock the enhancing mechanism for Li diffusion in Si/C. This understanding facilitates the modeling of batteries with composite anodes and will guide the corresponding structure designs for robust and high-energy-density batteries.