Improvements concerning the capacity and rate-capability of battery systems can not only be achieved by choosing suitable materials, but also by tailoring the electrode morphologies. Thus, a simulation study is performed to understand the influence of various microstructural properties such as particle size, porosity, and tortuosity on the transport mechanism. In this work, the classical Cahn–Hilliard model is extended to a multiple particle model system. We consider ellipsoid-like particles as an example, however, the model can be readily applicable to particles of complicated geometries. According to the diffusional properties of electrode and electrolyte, a study is conducted on transportation rate dependence with the electrode structures. Under Dirichlet conditions for concentration, simulation results predict a linear dependence of the characteristic time on tortuosity. These lines are converging with variation in particle size at higher tortuosity values, while they are diverging with variation in porosity. Furthermore, the results suggest that systems consisting of smaller particles are limited by surface reaction while larger particles tend toward the bulk-transport limited theory derived for planar electrodes.