The past decades have witnessed an increasing interest in numerical simulation for flow in fractured porous media. To date, most studies have focused on 2D or pseudo-3D computational models, where the impact of 3D complex structures on seepage has not been fully addressed. This work presents a method for modeling seepage in 3D heterogeneous porous media. The complex structures, typically the stochastic discrete fractures and inclusions, are able to be simulated. A mesh strategy is proposed to discretize the complex domain. In particular, a treatment on the intersected elements is developed to ensure a conforming mesh. Then, numerical discretization is provided, in which the flux interactions of fractures, inclusions and surrounding rock matrix are included. Numerical tests are performed to analyze the hydraulic characteristics of 3D fractured media. First, the developed framework is validated by comparing numerical solutions with the results of embedded discrete fracture model. Next, the effects of orientation, aperture and radius of fractures on fluid flow and equivalent permeability tensor are analyzed. The variations of pressure distribution are studied in heterogeneous and homogeneous media. Finally, the hydraulic properties of a medium with complex structures are investigated to show the difference of hydraulic feature between fractures and inclusions.