Coal mining processes produce large amounts of dust particles that seriously pollute the environment and threaten health. Spraying technology is a primary technique for dust removal. To date, experimental methods are mainly applied to study the atomization and dust removal properties of water droplets, but the intermolecular mechanism involved is unclear. First, a test platform was assembled to evaluate the atomization and dust removal performance of APG12/active water. Then, APG12 droplet and APG12 droplet/anthracite molecular models were constructed, and the underlying mechanism was elucidated through molecular simulation. The experimental results showed that the droplet diameter of the APG12/active water spray decreased by 14.15%, and the dust removal efficiencies of total dust and respirable dust increased by 39.55% and 61.51%, respectively. The simulation results indicated that APG12 molecules and H2O molecules exhibited attractive interactions. This interaction weakened the electrostatic attraction between the H2O molecules in the APG12/active water droplets. Moreover, the interaction enhanced the repulsive van der Waals interactions, reduced the number of hydrogen bonds, and increased the diffusion coefficient of H2O molecules. As a result, the droplets were relatively easy to break. In addition, APG12 molecules covered the surfaces of anthracite molecules, thus increasing the surface oxygen content and the electrostatic attraction, van der Waals forces and hydrogen bonding between H2O and coal molecules. This enhancement, in turn, improved the wettability of coal dust. Herein, the molecular mechanism of dust removal from APG12/active water was analysed, providing guidance for the development of new dust suppressants.