In this paper, the electrochemical properties of c-Si/a-Si lithiation and c-Li3.75Si/a-Li4.5Si delithiation processes are reproduced by using GCMC and DeePMD. Our simulations capture the qualitative features of the lithiation/delithiation processes of Si anodes, and we obtain a series of amorphous configurations in meta-stable states, providing new insights for the reaction mechanism under different charging/discharging paths. (1) In the process of c-Si/c-Li3.75Si destruction and a-LixSi phases formation, the rapid jumps of formation energies and voltage curves are observed. The former corresponds to the transformation of crystal to the Li-Si solid solution and then to the a-LixSi phase, while the latter corresponds to the c-Li15-δSi4-like to the a-LixSi phases. The formation energy of c-Li3.75Si to a-LixSi phase during Li removal (0.25 eV) is higher than that of c-Si to a-LixSi phase during Li insertion (0.10 eV). ( ) The voltage plateaus in the initial stage of the c-Si and a-Si lithiation are reproduced by our simulations with a predicted voltage plateau difference of 0.17 V, which is comparable to the experimental value of 0.22 V. The successful prediction of the experimentally observed two-phase region in c-Si and a-Si is further justification for the computational scheme employed in this work. Different formation energy profiles of a/c-Si systems lead to different Li contents in the a-LixSi endmember of the two-phase region, which also matches well with previous experimental observations of the a-LixSi phase with different Li content. (3) The simulation estimates that the latent heat from c-Li3.75Si to a-Li3.75Si phases is 0.26 eV, which quantitatively agrees with experimental measurements. In addition, the simulations show that there is a kinetic obstacle to converting a-Li3.75Si phase into c-Li3.75Si phase.