This study aims to explore changes in the microstructure and wettability of water-containing coal after hot flue gas (CO 2 −N 2 ) injection. To achieve this aim, thermal modification was conducted on Wulan anthracite with the aid of an experimental platform for coal modification by hot flue gas injection, and changes in the microscopic characteristics before and after the modification were investigated by means of Fouriertransform infrared spectroscopy (FT-IR) and carbon-13 nuclear magnetic resonance ( 13 C NMR). The results demonstrate that affected by acidic and hydrothermal environments, some oxygencontaining functional groups and aliphatic side chains in the molecular structure become detached. To be specific, the coefficient of oxygen-containing functional groups I O declines by 19.3%, and the aliphatic carbon content f al decreases by 32.7%. With the obtained microscopic data, the coal macromolecular structure models before and after the modification were established and verified by inverting the 13 C NMR spectra, and the coal matrix models with a projection area of 100 nm 2 were also generated. Subsequently, the wetting behavior of a water cluster on the coal matrix model was simulated by a molecular dynamics method. Based on the simulation results, a method of characterizing the microscopic wettability according to the maximum spreading area H and the maximum height D was put forward. The results are pretty consistent with the experimentally measured wettability. These results can lay a foundation for researching the microscopic control mechanism of water-containing coal seam modification by hot flue gas injection.