Carbon graphite has received much attention over the last decades as the best candidate for negative Li-ion battery electrodes due to its thermal stability and optimal cycling capability. This paper aims to give a comprehensive account of the effect of microstructure morphology such as porosity, tortuosity, solid-electrolyte interface area and active material particle geometry on the overall performance of an electrode. Simulated annealing method (SAM) was used to reconstruct a virtual microstructure of a graphite anode based on different active material particle configuration. The underlying species transport and reaction kinetics of an electrochemical cell were modeled through an electrical circuit composed of different components. Simulated results show that active material particle geometry directly influences the tortuosity and specific surface area of the microstructure, thus affects the solid and electrolyte phase electronic/ionic mobility. Nyquist plot provided an overall impedance of ionic and electronic diffusion over a frequency range of 0.1 mHz to 20 kHz. The semi-circle in the high-frequency region is associated with charge transfer resistance and dielectric behavior of the solid electrolyte interface (SEI) while the 45 degrees slope at the low-frequency region is a result of lithium diffusion into the solid electrode.