In order to realize Si as a negative electrode material in commercial Li-ion batteries, it is important to understand the mixing mechanism of Li and Si, and stress evolution during lithiation in Si negative electrode of Li-ion batteries. Available experiments mainly provide the diffusivity of Li in Si as an averaged property, neglecting information regarding diffusivity of Si. However, if Si can diffuse as fast as Li, the stress generated during Li diffusion can be reduced. We, therefore, studied the diffusivity of Li as well as Si atoms in the Si-anode of Li-ion battery using an ab initio molecular dynamics-based methodology. The electrochemical insertion of Li into crystalline Si prompts a crystalline-to-amorphous phase transition. We considered this situation and thus examined the diffusion kinetics of Li and Si atoms in both crystalline and amorphous Si. We find that Li diffuses faster in amorphous Si as compared to crystalline Si, while Si remains relatively immobile in both cases and generates stresses during lithiation. To further understand the mixing mechanism and to relate the structure with electrochemical mixing, we analyzed the evolution of the structure during lithiation and studied the mechanism of breaking of Si-Si network by Li. We find that Li atoms break the Si rings and chains and create ephemeral structures such as stars and boomerangs, which eventually transform to Si-Si dumbbells and isolated Si atoms in the LiSi phase. Our results are found to be in agreement with the available experimental data and provide insights into the mixing mechanism of Li and Si in Si negative electrode of Li-ion batteries. © 2011 American Chemical Society.