Si-Ge composites have recently been explored as an anode material for lithium-ion batteries due to their stable cycle performance and excellent rate capability. Although previous reports show the benefits of Si-Ge composites on electrochemical performance, the specific mechanism and structural effects have been overlooked. Here, the structural effect of Si-Ge heterogeneous nanostructures on both mechanics and kinetics is systematically studied through theoretical analysis and detailed experimental results. Si-Ge and Ge-Si core–shell nanowires are employed for this study. The Si-Ge core–shell nanowires show a much improved electrochemical performance, especially cycle performance and rate capability, when compared to those of the Ge-Si core–shell nanowires electrode. On the basis of the detailed experimental results and associated theoretical analysis, its is demonstrated that the strain distribution and Li diffusivity and/or diffusion path are significantly affected by the Si-Ge heterostructure, which induce different mechanics and kinetics associated with lithium.