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Accurate prediction of the flow characteristics in low-permeable porous media is of great importance for achieving efficient geo-energy development as well as gas geological storage practices. Due to the microscale and complex geometry of the formation structures, mechanistic studies on the flow behavior in low-permeable porous media have arisen as a challenging research topic. In this paper, a pore-scale numerical study is carried out concerning the seepage characteristics in the low-permeable Berea core. After extracting the complex pore structure from the high resolution CT images, a novel methodology is proposed to screen the simulation representative elementary volume (REV), on which the fluid flow characteristics in the low-permeable pore media are scrutinized with help of the comprehensive Computational Fluid Dynamics (CFD) software. The roughness effect, which becomes significant in microscale pore channels, is taken into account for the permeability result corrections. Based on good agreement between the pore-scale simulation and the macroscale measurement results, the capability of the proposed CFD workflow on the study of the seepage characteristics in low-permeable porous media is well demonstrated.