The transport of natural gas in shale resources is of multiscale and multiphysics nature. The gas transport involves dealing with pores of different length scales and geometrical orientation. Understanding and modeling the interactions of those pores are crucial for proper description of shale matrix deliverability and dynamics. These interactions are less understood at a microscopic scale during the depletion of shale reservoir. In this study, we consider transient flow behavior of a compressible fluid in organic nanoporous material with micro-fractures, or cracks, using a pore network modeling approach. We present a multistep workflow where the transport in the organic nanopores is studied considering the advective-diffusive-adsorptive mechanisms then, coupled with the microcracks for better understanding and optimizing of natural gas organic-rich shale. The natural gas is initially stored in the pore network at high pressure as free and adsorbed fluids and its pressure-driven viscous flow includes additional diffusion mechanisms. The percolation theory is used to obtain some approximations to the organic matrix flow regime coefficients. The organic materials-microcracks coupling term is derived and validated relating the flow rate exchange to the pressure difference with some modifications in order to account for the organic matrix transport dependency on the pressure. The coupling flow exchange term is used to link the local nanoscale heterogeneity to the large scale continuum modeling of shale reservoir. The upscaled model captures the transport exchange during the transient and steady-state flow conditions.