The evolutionary characteristics of pore structure from Permian marine-continental transitional shale were examined based on a suite of natural shale samples from the Ningwu and Qinshui Basins in northern China, which ranged in maturity from immature (vitrinite reflectance, Ro = 0.44%) to over-mature (Ro = 1.85%). Experiments included mercury intrusion, nitrogen adsorption, and carbon dioxide adsorption, and were conducted to quantify pore volume and pore size distributions. Samples with different thermal maturity had large differences in micropore, mesopore, and macropore volume and pore size distributions. Mesopore and macro pore volumes were the largest in immature shale and declined with increasing maturity to intermittent minima in the mature shale, continuing to increase to the over-mature shale. However, micropore volume gradually increased during maturation. The pore-related variances may be primarily controlled by maturity, whose effect was stronger than other factors (total organic carbon and mineral composition). During maturation, changes in pore size distribution and relative proportions of micropores, mesopores, and macropores were related to both chemical (transformation of organic matter into hydrocarbons) and mechanical (compaction) processes. Pore volume was reduced during the transition from immature to mature stage, likely mainly due to compaction instead of liquid hydrocarbon filling the pores, whereas the increase in pore volume during the transition from the mature to over-mature stage was mainly associated with the transformation of organic matter.