Nanoscale pores have been proven the major space for coalbed methane storage and important tunnels for coalbed methane transport. In this study, the influences of chemical composition, disorder degree and crystallite structure of coal macromolecule on the nanoscale pores were investigated by using different rank nature-matured coal samples via the methods of nuclear magnetic resonance (NMR), Raman spectroscopy, X-ray diffraction (XRD), low-pressure CO2 adsorption experiment and N-2 adsorption experiment. The results show that the volumes of 0.4-1.1 nm pores in naturally-matured coals show strong correlations with coal crystallite structure and chemical composition, but a weak correlation with disorder degree of coal molecule. In contrast, the volumes of 2-150 nm pores have a good correlation with disorder degree of coal molecule, but have weak correlations with the crystallite structure and chemical composition. When aromatic carbon ratio is smaller than 63%, the volume of 0.4-1.1 nm pores decreases with increasing the aromatic carbon ratio of coal molecules. Beyond that, the volume of 0.4-1.1 nm pores continues increasing with an increase in the aromatic carbon ratio. In addition, when the vitrinite reflectance (R-o) of the coal samples is > 0.7%, volume of 0.4-1.1 nm pores increases with increasing the average lateral size (L-a) and stacking height (L-c). The effects of chemical composition and crystallite structure on 0.4-1.1 nm pores of naturally-matured coal samples obtained in this study are consistent to those of artificially-matured coals in our previous study (Liu a al., 2018). Based on the Raman data, the effect of disorder degree of coal molecule on nanoscale pores was also investigated. With D-1/G ratio increasing, volume of 2-150 nm pores increases gradually. Considering that 0.4-1.1 nm pores are mainly related to the characteristics of single basic structural unit (BSU) (L-a, L-c and chemical composition) and 2-150 nm pores are related to arrangement of different BSUs (disorder degree), it is thought that 0.4-1.1 nm pores are formed inner BSUs and 2-150 nm pores are formed in the space between different BSUs.