During overcharging of lithium-ion batteries, lithium plating can occur on the anode surface when the maximum lithium intercalation concentration is exceeded, while the cathode is in a lithium-poor state, which can result in shortened battery lifespan and safety. In this work, the geometric structure of the positive electrode particles is designed based on the tomography data, while the negative electrode particles are represented by spheres with different sizes. The homogenization method is used, with the carbon filler, binder and electrolyte regarded as a single porous conductive adhesive domain. Based on the main mechanism of lithium-ion battery overcharge, a coupled three-dimensional electrochemical-mechanical-thermal overcharge model on a particle scale is developed for NCM cathode and graphite anode. The coupled mathematical model consists of four parts, namely the electrochemical model, the lithium plating model, the thermal model and the stress-strain model. In terms of lithium precipitation, the particle radius parameter and charging rates are investigated. The results show that the lithium plating concentration of the particles near the separator is higher, following the “principle of proximity” , namely the sequence of lithium deintercalation is related to the migration path. The surface of anode particles with small particle size is more prone to lithium precipitation due to the high maximum lithium ion concentration on the surface of the particles, the low surface lithium precipitation overpotential, and the high average Von Mises stress. At high charging rate, fast charge transfer rate and ion diffusion rate result in a low voltage at the anode, triggering off lithium precipitation. At a low rate, polarization and low temperature can lead to the precipitation of more lithium on the surface of the anode particles. In terms of stress, the spatial distribution between particles and thermal effects are investigated. The ratio of the distance from the contact surface to the center of the particle to the particle radius is calculated and defined as the contact depth ($ J_{\rm r} $), in order to better describe the law of particle contact stress. It is shown that the contact depth between particles is inversely proportional to the stress on the contact area. When the heat generation effect is considered, the temperature of the battery rises faster with the increase of the charging rate. The electrochemical parameters related to temperature and the lithium concentration diffusion gradient increase significantly, and the influence of temperature on the particle stress is also more significant. The relevant results can provide theoretical basis and guidance for designing battery and optimizing charge strategies.