In order to study the wetting mechanism of imidazole ionic liquids on lignite surfaces, molecular dynamics simulations combined with quantum chemistry were used to analyze the molecular level of 1-butyl-3-methylimidazolium chloride salt ([Bmim][Cl]), 1-butyl-3-methylimidazolium tetrafluoroborate ([Bmim][BF4]), 1-ethyl-3-methylimidazolium tetrafluoroborate ([Emim][BF4]) adsorption and wetting processes on the surface of lignite molecules. The electrostatic potentials and frontline orbital energy levels of [Bmim][Cl], [Bmim][BF4], and [Emim][BF4] and coal molecular models were analyzed to determine their nucleophilic and electrophilic regions based on the density flooding theory (DFT) in Gaussian 09 program. The water-coal system and ionic liquid–water-coal system were constructed from a microscopic perspective by dynamics simulations, and the relative concentration distribution of each system in the z-axis direction, the diffusion coefficients of water molecules in each system, and the non-bonding interactions of each system were analyzed. The results showed that [Emim][BF4] has the largest front-line orbital energy polarity and the best wettability for coal. [Emim][BF4] was more likely to interact with water molecules to form hydrogen bonds and had the highest number of hydrogen bonds with water molecules. The molecular dynamics simulations revealed that the adsorption of ionic liquids on the surface of lignite increased the adsorption thickness between water-coal systems, which led to a more extensive diffusion of water molecules, which increased the negative interaction energy between water-modified lignite and further improved the hydrophilicity of lignite, with [Emim][BF4] molecules having the strongest ability to improve the hydrophilicity of lignite. These results further demonstrated that [Bmim][Cl], [Bmim][BF4], and [Emim][BF4] can significantly improve the wettability of coal dust, which was important for improving the effect of coal seam water injection and reducing the dust concentration.