Inhibition mechanism of three purine compounds, adenine (A), 2-amino-6-thiol-9H-purine (B) and 2,6-dithiol-9H-purine (C), was investigated by quantum chemical calculation and molecular dynamic simulation. The molecular reactivity was studied by quantum chemical calculation, and the distribution of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), the energy gap between HOMO and LUMO and the Fukui index were proposed to describe the active sites of molecules, and the inferred inhibition efficiency followed the order of A , B , C. Furthermore, the adsorption behaviour of these three purine molecules on a metal surface was investigated via molecular dynamics simulation. The analysis of adsorption configuration indicated that these three purine molecules adsorbed parallely onto the metal surface, and the inferred inhibition efficiency from interaction energy also followed the order of A , B , C. These inferred inhibition efficiency from theoretical calculation was in good accordance with experimental results. This accordance indicated that our proposed theoretical method might be a feasible approach to assess the inhibition performance of inhibitors. Moreover, our research was helpful to filter the aimed inhibitor and design of the new inhibitor.