Understanding the fundamental processes at the electrode/electrolyte interface during charge and discharge will aid the development of high-capacity Li-ion batteries (LIBs) with long lifetimes. Finite Element Methodology studies are here used to investigate the interplay between morphological changes and electrochemical performance in Si negative electrodes. A one-dimensional battery model including Solid Electrolyte Interphase (SEI) layer growth is constructed for porous Si electrodes in half-cells and used for simulating electrochemical impedance response during charge and discharge cycles. The computational results are then compared with experimental investigations. The SEI layer from the electrolyte decomposition products, different depending on the presence or absence of the fluoroethylene carbonate (FEC) additive, covers the electrode surface porous structure and is leading to an increasing polarization observed in the Nyquist plots during cycling. A continuous reformation of the SEI layer after each cycle can be observed, leading to consumption of Li+. The electrolyte composition also results in a variation of electrode porosity, which affects the performance of the cell. A more stable porous network is formed when using the FEC additive, rendering a reduction in polarization due to improved Li diffusion inside the electrode composite.