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Investigation of the resident site and the adsorption phase structure of thiolates is of fundamental importance for understanding the formation of self-assembled organic monolayers on metal substrate surfaces. In the present study, we have investigated adsorption of methanethiol, CH3SH, on the ferromagnetic Co (0001) surface using density functional theory calculations.We find that the dissociative adsorption of CH3SH forming an adsorbed methylthiolate (CH3S) and an adsorbed H atom is energetically favorable, and that the CH3S molecule adsorbed at the threefold fcc and hcp hollow sites is most stable. The adsorption energy at the bridge site is only ~ 0.2 eV smaller than that at the threefold hollow site, and the adsorption of CH3S at the atop site is unstable. For the (√3 × √3)R30°, (2 × 2) and (2 × 3) adsorptions, we find that the S-C bond tends to be normal to the surface, whereas for the s231d adsorption it tilts away from the surface normal direction by ~ 40°. The (2 × 1) adsorption phase is much less stable. The reduction of the adsorption energy with the increasing coverage is attributed to the repulsive interaction between the adsorbates. Our calculations show that the (√3 × √3)R30° structure may form in the process of methylthiolate adsorption on Co (0001) due to its adsorption energy being only 0.1 eV lower than that for the (2 × 2) and (2 × 3) structures. We find that there is a charge transfer from the substrate surface atoms to the S atoms, and that the S-Co bond is strongly polar. The surface Co atoms bound to S have a magnetic moment of ~ 1.66μB, while the surface Co atoms unbound to S have a larger magnetic moment of ~ 1.85μB. The S atom in the adsorbed CH3S acquires a magnetic moment of ~0.08 μB.