Context <p>This study systematically investigated the molecular structure of Guizhou Longfeng anthracite to provide theoretical support for its efficient and clean utilization. Its two-dimensional planar and three-dimensional aggregated molecular model was constructed using proximate/ultimate analysis, Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and solid-state ¹³C nuclear magnetic resonance (¹³C-NMR), combined with ChemDraw and Material Studio software. The constructed molecular model was then validated through multi-dimensional comparison of experimental and simulation results, followed by detailed gas diffusion behaviour simulation. Results showed that the molecular formula of C₁₈₀H₁₀₆O₁₀N₂S was derived for LF coal, and its lowest-energy configuration of the aggregated molecular model was obtained via molecular mechanics and dynamics optimization in Material Studio. Simulated density and porosity deviated from experimental results by 1.45% and 1.77%, respectively; the relative errors of CO₂ and CH₄ saturation adsorption capacity were 2.42% and 4.17%, confirming the model’s rationality. Additionally, gas diffusion in the coal molecular model was substantially enhanced with increasing temperature, with a more pronounced enhancement effect for CH₄ than for CO₂.</p> Methods <p>The 2D model was built with ChemDraw. The 3D model geometry optimization was performed with the Forcite module (Dreiding force field, QEq charges) in Material Studio. Annealing was performed under the NVT ensemble at temperatures ranging from 300 to 600&#xa0;K. An aggregated model was constructed using the Amorphous Cell module. Validation was performed by comparing simulated density, porosity (Connolly surface), and GCMC-simulated CO₂/CH₄ adsorption with experimental data. Gas diffusion was simulated via molecular dynamics.</p>