To investigate the effect of carbon defects on the hydrophilicity of the whole surface of the coal pyrite, the adsorption of the single H2O molecule at different sites of the coal pyrite surface was studied with the DFT calculation. It was found that, like the ideal pyrite, the single H2O molecule can stably adsorb at the doping-position, the ortho-position and the meta-position of the coal pyrite. The covalent bond and anti-bond were formed between O (water molecule) and Fe (the coal pyrite) through the Fe 3d orbital and O 2p orbital. Meanwhile, the S–H bond was replaced by the C–H bond. But away from the carbon defect centre, the adsorption of the single H2O molecule increased gradually and the Fe–O covalent bond strength between the single H2O molecule and the pyrite strengthened, which eventually became close to that of the undoped coal pyrite surface.