A mesh mapping method is proposed to incorporate stress effect into the hydraulic analysis for highly fractured rock masses. Mechanical and hydraulic mesh are introduced for the hydraulic and mechanical simulations, respectively. The mechanical mesh contains strong discontinuities for capturing the fracture opening, closure and shearing, while the hydraulic mesh only consists of merged triangles on fractures. Using finite element method and unified pipe network method, stress effects on the equivalent permeability of complex discrete fracture networks (DFNs) are studied. The numerical result demonstrates that the mesh mapping method is effective to the stress-dependent analysis of 3D complicated DFNs.