The geothermal reservoir rock has poor diagenesis, loose cementation, sand-mud interbedded structure, large difference in physical properties, strong heterogeneity and complex pore structure. The reservoir damage caused by particle migration makes the development of geothermal reservoir more difficult. At present, it is urgent to clarify the influence of pore structure on geothermal reservoir seepage. In this paper, the mineral composition and pore structure of core thin sections were observed under a polarizing microscope, and the relevant parameters for quantitative characterization of pore structure were extracted. Through indoor core flow experiments, the seepage law of geothermal reservoir fluid under different experimental conditions is studied, and the influence of pore structure on reservoir rock seepage is analyzed. The results show that the sorting coefficient of geothermal reservoir is 1.51–3.15. There are great differences in pore structure between sandstones of different lithologies. The pores of medium sandstone are well developed, providing more reservoir space and seepage channels. The pore structure has a significant effect on the seepage capacity of geothermal reservoir. In the development of geothermal reservoirs, fully grasping the pore structure characteristics of sandstone and its influence on seepage characteristics has important guiding significance for efficient recharge and exploitation of geothermal reservoirs.