Si is an attractive material for anodes in Li ion batteries because of high specific capacity. However, it undergoes significant volume change during electrochemical reactions, causing mechanical fractures and capacity decay, which is a serious bottleneck for commercialization. Despite several research attempts to understand the stress evolution in Si, the process remains unclear. A fundamental study of the initial formation of the Li–Si alloy is hence necessary for a better understanding of the stress evolution. In this study, the nucleation and growth of Li–Si alloys on various crystalline Si (c‐Si) surfaces during lithiation is observed by the authors. Distinct Li–Si alloys are formed with square pyramid, triangular pyramid, and circular bump shapes on the {100}, {111}, and {110} surfaces, respectively. These unique structures are caused by the preference for Li insertion on the c‐Si surface and are maintained even after further growth of the alloy at the outermost layer. The particular structures are assumed to cause a different degree of stress at the reaction front during lithiation. The authors expect that this fundamental study will contribute to an optimal design of the Si anode based on the better understanding of the type of stress present at each c‐Si.