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The three-dimensional (3D) structures of pores directly affect the CH4 flow. Therefore, it is very important to analyze the 3D spatial structure of pores and to simulate the CH4 flow with the connected pores as the carrier. The result shows that the equivalent radius of pores and throats are 1–16 μm and 1.03–8.9 μm, respectively, and the throat length is 3.28–231.25 μm. The coordination number of pores concentrates around three, and the intersection point between the connectivity function and the X-axis is 3–4 μm, which indicate the macro-pores have good connectivity. During the single-channel flow, the pressure decreases along the direction of CH4 flow, and the flow velocity of CH4 decreases from the pore center to the wall. Under the dual-channel and the multi-channel flows, the pressure also decreases along the CH4 flow direction, while the velocity increases. The mean flow pressure gradually decreases with the increase of the distance from the inlet slice. The change of mean flow pressure is relatively stable in the direction horizontal to the bedding plane, while it is relatively large in the direction perpendicular to the bedding plane. The mean flow velocity in the direction horizontal to the bedding plane (Y-axis) is the largest, followed by that in the direction horizontal to the bedding plane (X-axis), and the mean flow velocity in the direction perpendicular to the bedding plane is the smallest.