To investigate the molecular structure and micropore structure of organic matters in coal-measure shale, the black shale samples of the Shanxi formation were collected from Xishan Coalfield, Taiyuan, and a hybrid experimental–simulation method was used for realistic macromolecular models of organic matter (OM). Four experimental techniques were used to determine the structural information of OM, including elemental analysis, state13C nuclear magnetic resonance (13CNMR), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared spectroscopy (FTIR). With structural parameters, two-dimensional (2D) average molecular models of OM were established as C177H160O8N2S with a molar weight of 2474, which agreed well with the experimental13C-NMR spectra. A realistic three-dimensional (3D) OM macromolecular model was also reconstructed, containing 20 2D molecules with a density of 1.41 g/cm3. To determine the connectivity and spatial disposition of the OM pores, focused ion beam microscope (FIB-SEM) and transmission electron micrographs (TEM) were utilized. The 3D OM pores models were developed. The results show that whether the OM pores varied from 20 to 350 nm as obtained from FIB-SEM images or less than 10 nm as observed in the TEM images, both were of poor connectivity. However, the ultra-micro pores from the 3D OM macromolecular model varied from 3Å to 10 Å and showed certain connectivity, which may be the main channel of diffusion. Furthermore, with the pressure increased, the methane adsorption capacity of the 3D OM model increased with a maximum value of 103 cm3/g at 7 MPa, indicating that OM pores less than 1 nm have a huge methane adsorption capacity. Therefore, our work provides an analysis method that is a powerful and superior tool in further research on gas migration.