To develop high-capacity Li-ion batteries, volume expansion and material degradation of Si anodes have been attracting increasing attention. However, the effects of phase structures and geometrical constraints on the failure mechanism of lithiated Si have not been well understood. Considering phase boundaries formed during electrochemical cycles, we conducted molecular dynamics simulations to investigate the failure behaviour and microstructural evolution of single-phase and dual-phase (core–shell) lithiated Si structures when subjected to biaxial tensile stress. During lithiation, lithiated Si structures show a brittle-to-ductile transition. The brittle fracture is associated with nanoscale cavitation and void propagation. The ductility of lithiated Si structures increases with Li content due to the rearrangement of Li atoms. Compared with single-phase lithiated Si, dual-phase structures tend to fracture owing to inhomogeneous deformation and nanoscale cavitation. On the other hand, the ductility of lithiated Si decreases during delithiation, especially in dual-phase structures. This work provides a better understanding of the structure–property relationship of lithiated Si in charging-discharging cycles and strategies to improve the electrochemical performance of Si-based electrodes.