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Pore structure characterization and its effect on methane adsorption on shale kerogen are crucial to understanding the fundamental mechanisms of gas storage, transport, and reserves evaluation. In this study, we use 3D scanning confocal microscopy, scanning electron microscopy (SEM), X-ray nano-computed tomography (nano-CT), and low-pressure N2 adsorption analysis to analyze the pore structures of the shale. Additionally, the adsorption behavior of methane on shales with different pore structures is investigated by molecular simulations. The results show that the SEM image of the shale sample obviously displays four different pore shapes, including slit pore, square pore, triangle pore, and circle pore. The average coordination number is 4.21 and the distribution of coordination numbers demonstrates that pores in the shale have high connectivity. Compared with the adsorption capacity of methane on triangle pores, the adsorption capacity on slit pore, square pore, and circle pore are reduced by 9.86%, 8.55%, and 6.12%, respectively. With increasing pressure, these acute wedges fill in a manner different from the right or obtuse angles in the other pores. This study offers a quantitative understanding of the effect of pore structure on methane adsorption in the shale and provides better insight into the evaluation of gas storage in geologic shale reservoirs.