A better understanding of lithium-silicon alloying mechanisms and associated mechanical behavior is essential for the design of Si-based electrodes for Li-ion batteries. Unfortunately, the relationship between the dynamic mechanical response and microstructure evolution during lithiation and delithiation has not been well understood. We use molecular dynamic simulations to investigate lithiated amorphous silicon with a focus to the evolution of its microstructure, phase composition, and stress generation. The results show that the formation of LixSi alloy phase is via different mechanisms, depending on Li concentration. In these alloy phases, the increase in Li concentration results in reduction of modulus of elasticity and fracture strength but increase in ductility in tension. For a LixSi system with uniform Li distribution, volume change induced stress is well below the fracture strength in tension.