Nanostructured silicon anodes, which possess extremely high energy density and accommodate large strain without pulverization, have been developed rapidly for high-power lithium ion batteries. Here, using in situ transmission electron microscopy, the lithiation behavior of silicon nanowires with diameters smaller than 60 nm was investigated. The study demonstrated a direct dependence of the self-limiting lithiation on the pristine diameter. A "punch-through" lithiation process at the core of nanowires with pristine diameters slightly larger than the self-limiting threshold is suggested to occur with the consequent formation of a stage structure. Our work demonstrates the crucial role of mechanical stress and local defects in determining the migration and geometry of the reaction front at the mesoscopic scale. This intriguing finding holds critical significance for the application of silicon nanostructures in high-power lithium ion batteries.