Electrical and mechanical properties of gold‐ para ‐benzenedimethanethiol (BDMT)‐gold molecular junctions with different binding configurations have been investigated using density functional theory (DFT) combined with a non‐equilibrium Green’s function (NEGF) approach. We first determined the most stable structure in total electronic energy by geometry optimization of the molecular junction. We then studied how different stretching processes affect the conductance and the stretching forces. Particularly two stretching modes can bring about different conductance behavior. When only a single‐end molecular contact in interfacial configurations at the top and bridge sites is stretched, the molecular conductance first decreases exponentially. This is followed by a flat platform, and finally produced an abrupt conductance drop from the fracture of interfacial chemical bond Au‐Au. In the junction with a double‐end stretching mode, the fracture of Au‐S bond occurs either between the sulfur‐bonded gold atom and the underlying Au surfaces, or at either of the two Au‐S bonds in the double‐end stretching mode at the top‐pyramidal site. The latter interfacial structure consists of a four‐Au‐atom pyramidal structure adsorbed on gold surface, resulting in a sharp conductance increase just before complete fracture. This is closely associated with resonance tunneling of beta spin electrons in the critical breaking state of interfacial Au‐S bonds in gold‐BDMT‐gold molecular junction.