As a critical fossil energy, lignite has a huge resource, wide distribution, and a low comprehensive utilization rate. Investigations regarding the molecular structure model of lignite are beneficial for pre-judging the chemical reaction mechanism and reaction path of lignite in pyrolysis, liquefaction and gasification, thereby improving its comprehensive utilization. Eshan lignite was studied by Fourier transform infrared spectroscopy, ¹³C Nuclear magnetic resonance spectroscopy and X-ray photoelectron spectroscopy in this paper. Moreover, the structural unit parameters of carbon, oxygen and nitrogen of Eshan lignite were obtained. According to these parameters, the molecular structure model of Eshan lignite was established and optimized by using the quantum chemical modeling method in the Gaussian 09 computing platform. The results indicate that the content of aromatic carbon and aliphatic carbon is 39.20% and 49.51%, respectively. In detail, the aromatic carbon structure mainly includes benzene and naphthalene, and the ratio of aromatic bridgehead carbon to surrounding aromatic carbon is 0.07. The aliphatic carbon structure mainly contains methylene, methyl and oxy-aliphatic carbon. Furthermore, the oxygen atoms mainly exist in hydroxyl, ether oxygen, carboxyl and carbonyl. Moreover, the nitrogen structure mainly involves pyridine. Based on the results of ultimate analysis and ¹³C nuclear magnetic resonance spectroscopy analysis, the molecular formula of Eshan lignite was calculated as C₁₅₃H₁₃₇O₃₅N₂ after eliminating the influence of water by thermogravimetric experiment. The initial structural model of Eshan lignite was constructed via the connecting structural unit. The PM 3 basis set of semi-empirical method and density functional theory M06-2X/3-21G basis set were used to optimize the initial molecular configuration. The optimized model has obvious three-dimensional characteristics. Among these, the aromatic rings arrange irregularly in space, and the distance between every aromatic ring is far. The aromatic carbon structures are mainly connected by methylene, ether oxygen, carbonyl ester and aliphatic ring. The oxygen functional groups mainly distributed at the edge of molecular and aliphatic structures possess many side chains. The simulated infrared spectrum of the molecular model was obtained by analyzing the vibration frequency of the optimized molecular model, and it agrees with the experimental infrared spectrum well, representing the accuracy and rationality of the molecular structure model of Eshan lignite. This molecular structure model is conducive to understanding the physicochemical properties of Eshan lignite more intuitively and revealing its macroscopic properties. Meanwhile, the molecular structure model can provide a theory basis for further research on lignite pyrolysis, liquefaction and gasification.