Surface atom functionalization and the variation of aliphatic/aromatic structures within coal macromolecules are key factors to determine the pore structures within coalification. Here, the characteristics of nano-micron scale pore structures in coal were analyzed with the aid of coupled fluid intrusion and molecular probe technologies. Results indicate that the cleavage of long-chain aliphatic structures enhances the size of the pore throat and reduces the specific surface area (SSA) and pore volume (PV) of the mesopores (2-50 nm) when the third coalification jump occurs. Macropores (> 50 nm) were slightly impacted by coalification and their development was primarily controlled by the diagenesis process, where macropores are gradually compacted and transformed into mesopores. Micropores (< 2 nm) overall increase with the enhancement of aromatization and condensation polymerization, however, in the stage of low volatile bituminous, the blocking of minerals or low boiling hydrocarbon solids will temporarily reduce micropores. Meanwhile, similar surface structures and functional groups lead to similar characteristics of the pore size distribution for mesopores and micropores. Furthermore, the peak value of microporous PV migrates to the smaller pore size and pore of < 0.4 nm in size generated from clearances among the aromatic layers gradually becomes dominant with the enhancement of condensation polymerization reaction. Results of fractal theories show that coalification has no effect on the fractal dimension (Df1) of macropores while a positive effect was discovered on Dv2 of mesopores and Dm of micropores. The heterogeneity and surface roughness of micropores and mesopores are controlled by coalification. Dv1 of mesopores is affected by diagenesis. Molecular probe analysis for atoms of pore walls suggests that the pore walls are contributed by aliphatic structures before the third coalification jump. Moreover, micropores among aliphatic structures developed relatively independently and small-scale pore networks frequently exist within them. With the enhancement of coalification accompanied by the cleavage of aliphatic structures, the aliphatic structures around the pore walls will be gradually replaced by the aromatic structure. Micropores of relative independence are decreased, and large-scale pore networks are gradually formed. Furthermore, the pore morphology developed more complex and strongly heterogeneous. High-density oxygen/nitrogen/sulfur functionalization will increase the micropores.