Quantum chemical calculations based on density functional theory (DFT) methods were performed on indigo blue (IB), methylene blue (MB), and crystal violet (CV) molecules as inhibitors for iron corrosion in acid media. DFT calculations were performed on the molecular structures to describe electronic parameters which are associated with inhibition efficiency such as the Homo values −4.981 eV, −4.518 eV, and −3.872 eV which increased in the order IB > MB > CV while LUMO values were −3.73 eV, −3.63 eV, and −2.87 eV for IB, MB, and CV, respectively. Quench molecular dynamics simulations performed at metal/vacuum interface were applied to find the equilibrium adsorption configurations and calculate the minima interaction energy between inhibitor molecules and iron surface Fe(110). The theoretical order of inhibition efficiency of these dye molecules had a linear relationship with experimentally observed inhibition efficiency on iron corrosion in acid media. The electronic structures as well as reactivity elucidate parameters which could be practical in designing novel high-efficiency, cheap, and eco-friendly inhibitors by quantitative structure-activity relationship (QSAR) method.