Abstract: Molecular structure modeling and analysis can help gain a deeper insight into microscopic structure and reaction mechanism of coal. A systematic and comprehensive study is made of the molecular structure of the lignite of Jungar Mining Area by using the technologies like elemental analysis, Fourier-transform infrared spectroscopy (FTIR), solid-state nuclear magnetic resonance carbon spectroscopy (¹³C-NMR), and X-ray photoelectron spectroscopy (XPS) as well as molecular simulations, and building of the two-dimensional structure model of the coal. Through geometric optimization of the plane model using the software Material Studio 2020 as well as hydrosaturation treatment, structural optimization and annealing dynamics simulation, a 3D model is generated as a result of twisting of chemical bonds and significantly reduced energy. The density simulation is further carried out to determine the optimum density and construct an aggregate model based on relation of potential energy with density. As indicated by study result, the optimum density of the lignite X_\mathrmB \mathrmP is 0.12, and benzene ring dominates its aromatic structure; the oxygen atoms exist mainly in form of phenolic hydroxyl group while nitrogen elements are mainly distributed in the pyrrole structure; as the lignite has a comparatively low sulfur content, the influence of sulfur is ignored in the model; the tortional energy and Van der Waals enegy play a dominate role in the stability of structure of lignite; the model-determined optimum density is 1.1 g/cm³ which is in good agreement with the actually measured value; as revealed by the aggregate structure model fitted up with altogether 40 micromolecular models, and by the results of optimization of molecular mechanics and dynamics, the distortion and deformation of the aromatic lamellae are attributed to the interaction of intermolecular and intramolecular forces — a factor causing the lignite to become disordered in molecular structure. Through density simulation made in the paper, the reliability of the model is improved, and the research findings provide a solid theoretical basis for in-depth study of characteristics of lignite from the molecular perspective.