A numerical procedure for the evaluation of equivalent permeability tensor for fractured vuggy porous media is presented. At first we proposed a new conceptual model, i.e., discrete fracture-vug network model, to model the realistic fluid flow in fractured vuggy porous medium on fine scale. This new model consists of three systems: rock matrix system, fractures system, and vugs system. The fractures and vugs are embedded in porous rock, and the isolated vugs could be connected via discrete fracture network. The flow in porous rock and fractures follows Darcy's law, and the vugs system is free fluid region. Based on two-scale homogenization theory, we obtained an equivalent macroscopic Darcy's law on coarse scale from fine-scale discrete fracture-vug network model. A finite element numerical formulation for homogenization equations is developed. The method is verified through application to a periodic model problem and then is applied to the calculation of equivalent permeability tensor of porous media with complex fracture-vug networks. The applicability and validity of the method for these more general fractured vuggy systems are assessed through a simple test of the coarse-scale model.