Electricity storage is one of the major challenges of our time. Among the new technologies that enable maximum electricity storage in a small volume, lithium-ion batteries (LIBs) are currently among the best candidates. LIBs are based on the reversible exchange of lithium ions between a positive electrode (most often a lithium transition metal oxide) and a negative one (graphite for most of the current technologies), the driving force being the difference in electrochemical potential between both electrodes. For graphite, a lamellar material made of stacked graphene sheets, lithiation occurs by intercalation of lithium between the sheets, with no transport across them. The filling of the graphene layers occurs through different stages, which correspond to the periodicity of the filled layers (one in two, one in three, etc.). In this study, we seek to numerically model the dynamic of these stages on a mesoscopic scale. To do this, the time evolution of lithium concentration in each layer is described using a Cahn–Hilliard formulation, resulting in a multi-layer modeling framework. The chosen Gibbs free energy model depends on the contributions of all layers and involves intra- and inter-layer repulsion energy terms. The purpose of this presentation is to show the results obtained after extending the multi-layer model, initially established in two dimensions, to three dimensions. 3D simulations, compared to 2D, still capture the right growth modes, after spinodal decomposition, and go beyond 2D results by enabling a more realistic dynamics of the stage 2 and stage 3 domain evolutions, also with imposed current boundary conditions. In addition, we introduce the semi-implicit time scheme used in this study, as well as the Jacobian-Free Newton Krylov (JFNK) algorithm used to solve the equation. Those numerical choices are decisive to ensure the robustness of the 3D implementation, while maintaining reasonable computation time. Finally, perspectives on coupling with an Allen-Cahn equation describing the movement of graphite planes as a function of lithiation stages are presented.