We present a new three-dimensional finite element technique to solve efficiently flows in a representative porous volume with fibrous microstructures, which employs a fictitious domain method to deal with immersed microstructures and a mortar-element method to satisfy rigorously the tri-periodic boundary condition for the representative volume element. Through the extensive numerical simulations for various fiber and fabric architectures, we investigate the relationship between the permeability and fiber architectures in order to establish a reasonable approximation method in estimating the permeability of such complex 3D architectures. Specifically we discuss the applicability and the limitation of the macroscopic permeability averaging rule for those purposes, using the permeability of simple structural building blocks. Finally, we present the Kozeny constants of various microstructures for a wide range of the fiber volume fraction, which may facilitate simple permeability estimation of complex 3D porous structures using the Kozeny–Carman model.