Understanding the explosion-inhibition mechanism of methane/coal dust mixtures at the atomic level is crucial. This study employed ReaxFF-MD and DFT calculations to investigate the inhibitory effects of NH4H2PO4 and (NH4)2HPO4 on methane/coal dust explosions. The research examined macroscopic products, chemical bonds, key reaction pathways, and intermediate products. Furthermore, the evolution mechanism of coal molecules involved in the explosion-inhibition reaction was elucidated. The results indicate that NH4H2PO4 inhibits CO2 generation, while (NH4)2HPO4 enhances H2O production. Additionally, the inhibitors affect not only the initial reaction steps of CH4 but also absorb reactive radicals (•H/•O/•OH) and intermediate products (•CH3/CH2O). Compared to NH4H2PO4, the inhibition cycling reactions of (NH4)2HPO4 exhibit greater diversity. Increasing inhibitors’ mass fraction promotes competing reactions among free radicals, which diminishes the inhibition effect on CH4 dehydrogenation, leading to oscillations in explosion-inhibition efficiency. The inhibitors also delay the bond-breaking time for both the aliphatic bond and the ether-oxygen bridge of coal molecules, thereby prolonging the ring-opening reaction time of these molecules.