<p>The study in this paper shows that cycle number and crystal structure have a significant impact on the capacity and cycling performance of lithium-ion batteries. However, we need to further understand the detailed dynamics and continuity of the capacity decay mechanism induced by the number of cycles and crystal structure at the nanoscale. To address this issue, we used molecular dynamics simulations to investigate the microstructural development and deformation behavior of silicon anodes in an electric field. Our results show that an increase in the number of cycles leads to a significant volume expansion of the silicon electrode, which in turn leads to capacity loss, reduced cycling capacity, and decreased structural stability. The silicon crystal structure transforms from a diamond structure to an amorphous structure depending on the degree of lithification and delithification. Volume expansion of the silicon anode occurs due to the presence of a large number of nanoscale voids. As more cycles are performed, the transformation associated with nanogap nucleation caused by non-spontaneous diffusion processes leads to an irreversible loss of capacity in lithium-ion batteries. Our analytical model shows that the diffusion-induced stress is not only related to the position of the silicon anode but also to the cycling time.</p>