For the microstructure evolution pathways during lithiation/delithiation, our result reveals a series of intermediate a-LixSi phases that are consistent with experiments. During a-Si lithiation, the Si-Si bond breaks from large Si clusters to rings and Y clusters, then breaks into Si-Si dumbbells and isolated Si atoms. For example, the simulated a-Li3.62Si phase with 59 mV is similar to the experimental a-Li3.4Si with 60 mV . During c-Li3.75Si delithiation, the structure remains unchanged with Li removal when x > 3.0. The Li2.992Si also remains crystalline although some Si-Si dimers and Si-Si-Si bonds appear. This is similar to the Li-deficient c-Li15-δSi4 phase characterized by Ogata et al. Stress simulations reveal that c-Si has higher stress than a-Si with Li insertion in the a-LixSi