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.