Abstract: In this work, we performed the pulse-decay experiment on a fractured shale core and applied the 3D embedded discrete fracture model (EDFM) to simulate the experiment process. The irregularly rough fracture surface was depicted in detail using a 3D scanner. Then the fracture surface profile was imported in the discrete fracture network model to simulate the flow process in the fracture-matrix system realistically. History matching was efficiently performed to simultaneously obtain porosity and permeability for the matrix and fracture. Gas properties after applying nanopore confinement were obtained by modifying Sutton's viscosity correlation with sensitivity analysis on the pore diameter ranging from 2 to 50 nm. Nanopore confinement results in low matched permeability due to viscosity reduction in the matrix-only porous media. The fracture-matrix system complicates the interpretation of nanopore confinement impact on flow behavior in shale reservoirs. Different scenarios of the highly fractured and matrix-dominated systems were discussed in detail by constructing the digital twin model.