High heterogeneity and nonuniformly distributed multiscale pore systems are two characteristics of the unconventional reservoirs, which lead to very complex transport mechanisms. Limited by inadequate computational capability and imaging field of view, flow simulation cannot be directly performed on complex pore structures. The traditional methods usually coarsen the grid to reduce the computational load but will lead to the missing microstructure information and inaccurate simulation results. To develop a better understanding of flow properties in unconventional reservoirs, this study proposed a new upscaling method integrated gray lattice Boltzmann method (GLBM) and pore network model (PNM), accounting for the fluid flow in heterogeneous porous media. This method can reasonably reduce the computational loads while preserving certain micropore characteristics. Verifications are conducted by comparing the simulation and experimental results on tight sandstones, and good agreements are achieved. The proposed method is proven to be capable of estimating bulk properties in highly heterogenous unconventional reservoirs. This method could contribute to the development of multiscale pore structure characterizations and enhance the understandings of fluid flow mechanisms in unconventional reservoirs.