Lithium ion batteries experience diffusion-induced stresses during charge and discharge processes which can cause electrode failure in the form of fracture. Previous diffusion-induced stress models and simulations are mainly based on simple active material particle structures, such as spheres and ellipsoids. However, the simple structure model cannot reveal the stress development in a real complex lithium ion battery electrode. In this paper, we studied the diffusion-induced stresses numerically based on a realistic morphology of reconstructed particles during the lithium ion intercalation process. The morphology of negative and positive active materials of a lithium ion battery was determined using X-ray micro/nano computed tomography technology. Diffusion-induced stresses were simulated at different C rates under galvonostatic conditions and compared with spherical particles. The simulation results show that the intercalation stresses of particles depend on their geometric characteristics. The highest von Mises stress and Tresca stress in a real particle are several times higher than the stresses in a spherical particle with the same volume.