Heterostructures of silicon and carbon nanotubes (CNT) have been widely studied as Li-ion battery anodes. The focus of the current study is to investigate the role of silicon configurations on the mechanical integrity of the Si–CNT heterostructured anodes during electrochemical cycling. We hypothesize that void nucleation and growth in silicon during electrochemical cycling of Li can induce fracture and eventual failure. To test this hypothesis, we utilized a custom developed multiphysics finite element modeling framework considering the lithium diffusion induced elasto-plastic deformation of silicon. We systematically varied the silicon component configuration and enumerated the stress field within it for one complete electrochemical cycle. Resulting evolution of stress state reveals that reducing the mechanical constraints on Si reduces the plastic flow of the material, and thus possibility of void nucleation and growth. We find that the Si droplet configuration is mechanically stable while the continuous Si coating configuration is prone to void growth induced mechanical failure. Present analysis provides a mechanistic understanding of the effect of Si configurations in heterostructured electrodes on its mechanical integrity, which can help in design of next-generation hetersostructured electrodes with improved capacity retention.