 A new model that keeps all major advantages of the single-particle model of lithium-ion batteries (LIBs) and includes three-dimensional structure of the electrode was developed. Unlike the single spherical particle, this model considers a small volume element of an electrode, called the representative volume element (RVE), which represents the real electrode structure. The advantages of using RVE as the model geometry were demonstrated for a typical LIB electrode consisting of nano-particle LiFePO4 (LFP) active material. The three-dimensional morphology of the LFP electrode was reconstructed using a synchrotron X-ray nano-computed tomography at the Advanced Photon Source of the Argonne National. A 27 μm3 cube from reconstructed structure was chosen as the RVE for the simulation purposes. The model was employed to predict the voltage curve in a half-cell during galvanostatic operations and validated with experimental data. The simulation results showed that the distribution of lithium inside the electrode microstructure is very different from the results obtained based on the single-particle model. The range of lithium concentration is found to be much greater, successfully illustrating the effect of microstructure heterogeneity.