•The 2D structure model of Zhundong coal was obtained by a13C-NMR, FTIR, XPS.•The angle, atomic vibration, bond torsion and inversion of the 2D structure was optimized to obtain the 3D energy-minimum conformation.•The 2D structure was verified by using 13C-NMR simulation.•The 3D structure was verified by using FTIR simulation. Understanding the coal molecular structure is of paramount importance for the effective utilization of coal. In this paper, the molecular structure of Zhundong coal (ZD) was characterized by physical detection techniques, such as solid state 13C nuclear magnetic resonance spectroscopy (13C-NMR), fourier transform infrared resonance spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS). The occurrence and distribution of aromatic carbocyclic frameworks were analyzed by 13C-NMR. Based on the FTIR and XPS analysis, the existing forms and the length of the aliphatic chain, the substitution forms of aromatic carbocyclic rings, and different types of functional groups were confirmed. The aliphatic chains and functional groups were introduced into these aromatic carbocyclic frameworks, and the 2D molecular structures model of ZD with the molecular chemical formula as C179H124O21N4 were constructed. The simulated 13C-NMR spectra of which were consistent with the experimental spectra, indicating the accuracy of the 2D ZD molecular structure model. Efforts were made to obtain the energy-minimum conformation of the 3D molecular structure by molecular mechanics (MM) and molecular dynamics (MD). The simulated FTIR spectra of the model were in good agreement with the experimental results, which fully verified the accuracy of the ZD molecular structure. The molecular structure provides a deep reference to understand the structural characteristics of ZD coal at the molecular micro-scale, which would be helpful to understand the reactivity of ZD coal.