We propose an efficient simulation method of three-dimensional (3D) resin flow in laminated preform composed of multiple layers with different permeabilities at each layer. Because of the small thickness of each layer, a huge number of nodes are needed for 3D flow simulation if solid elements are adopted and full 3D simulation takes extremely long even by parallel computing. Instead of 3D solid elements, we propose multi-layered shell elements for 3D flow simulation with a short computing time. We describe the numerical formulation of multi-layered shell element method to consider the through-thickness flow as well as the planar flow. The accuracy and efficiency are evaluated by new dimensionless parameters defined in terms of preform permeability ratio and of the ratio of shell element size to the distance between the adjacent layers. Some simulation results are presented to demonstrate the advantages of the multi-layered shell element method for 3D flow simulation. © 2019 Elsevier Ltd