For an electrode of lithium-ion batteries (LiBs), packing active particles yields a very complex microstructure that largely affects the battery performance. This work develops and validates a 3D microstructure-resolved model to study the influence of the active particle size distribution, particle shape, and particle packing configuration. The results show that mixing large and small particles in a random manner can increase the volume fraction of active materials, leading to the highest energy density when the diffusion limitation in the electrolyte is weak. A layered manner with small particles near the separator gives the highest energy density when the diffusion limitation in the electrolyte is severe. A wide particle size distribution deteriorates the performance of LiBs, as the number of large particles increases, and these particles are difficult for the intercalation of lithium. The effects of particle size distribution would not be qualitatively but quantitatively changed by the diffusion limitation in the electrolyte. Besides, the particle shape with a small sphericity is beneficial for improving energy density due to the shorter diffusion path. These results should serve to guide the optimal design of LiB electrodes with high performance.