The paper describes a new approach of atomic simulation for silicon (Si) anisotropic wet etching using molecular dynamics (MD). The extended Tersoff potential was adopted as a potential function for MD, which was able to handle Si etching reaction with hydrogen (H) and oxygen (O) atoms. The potential function also made it possible to represent a transition of electric charge under chemical etching MD simulations as a function of atomic distance. Binding energies between Si, H and O atoms were statically calculated by the function, and they showed good agreement with previously reported experimental data. Finally, etching MD simulation of single crystal Si in water was carried out using the extended Tersoff potential for revealing the effect of hydrogen termination at the top of Si on the interaction between Si, H and O atoms.