Multiple coal seams and interbedded rock assemblages formed in vertical progression due to the influence of multiple stages of sea level transgressions. Based on mercury injection experiment, low temperature liquid nitrogen experiment, porosity and permeability experiment and breakthrough pressure experiment, the vertical variation characteristics of coal-bearing strata in Gujiao block are explained in detail. The results of the mercury injection and low temperature liquid nitrogen experiments show that the pore structure characteristics fluctuate with increasing depth in the strata, with fewer micropores followed by transition pores. The BET specific surface area and average pore diameter of the Shanxi Formation are generally larger than those of the Taiyuan Formation. Due to the continuous cyclic sequence stratigraphy changes, the porosity, permeability, breakthrough pressure and breakthrough time of the samples show a certain cyclicity. Within the same sequence, the porosity is larger, and the permeability is smaller near the maximum flooding surface. Although the permeability of the sandstone samples is higher, the porosity is lower, and the breakthrough pressure and breakthrough times are greater. The strata in the study area formed in an oxidized environment that was affected by freshwater, and the pore structure of different lithologies is quite different. After the formation of sandstone, the intergranular pores generally underwent filling with secondary quartz, clay minerals and organic matter, resulting in low porosity and permeability.