Based on the hybrid density functional theory, the relationship between geometric structure of 1,4-butanedithiol molecular junction and the electrodes force and the breaking process of the molecular junction are studied. The electronic transport properties of the molecular junction under different external forces are further investigated using the elastic scattering Green’s function method. The numerical results show that different interface configurations result in different rupture forces. The rupture force is about 1.75 nN when the terminal S atom is sited at the hollow position of Au(111) surface. However, the rupture force is about 1.0 nN when the terminal S atom links with one Au atom which is on the gold surface singly. And with the breakdown of the molecular junction, the single Au atom is pulled away from the gold surface by the terminal S atom. These two results are consistent with different experimental measurements respectively. The molecule is twisted under the electrode pressure and thus further induces the surface Au atom to glide on the gold surface. However, the processes of the molecule twisted by pressure and restored by pulling are two irreversible processes. The stretching force of electrode is 0.7–0.8 nN, and the conductance always shows a minimal value under different interface configurations and twisting states, which is consistent with experimental conclusion. The change of the coupling between the terminal atom and the electrodes induced by the electrode force is the main factor of influencing the conductance of the molecular system. The existence of bimolecular junction results in a small possibility of higher conductance values, which is probed by experiment under a stretching force of about 0.8 nN.