The adsorption of the methylthiolate (MT) on the as-rich GaAs (001) surface has been studied by using density functional theory (DFT) calculations with a three-dimensional periodic boundary condition. A complete characterization of structures and binding energies of the system consisting of MT and As-rich GaAs (001) surface is obtained. It is found that the most reactive binding site is related to empty Ga dangling bonds located at the three-fold-coordinated second-layer Ga atom. Moreover, electronic properties of these structures are also calculated to study the bonding characteristics of S-Ga and S-As bonding, which show that the covalent bonding of the former is stronger than that of the latter. The analysis for this shortest chain binding is helpful to realize the electrical passivation and chemical protection of GaAs surfaces.