The azobenzene molecular junction has aroused much interest of scientists due to its switching property arising from its photoinduced isomerism. Owing to the existence of the cis and trans isomers, the electronic transport properties of the azobenzene molecules are promised to show significant differences. The experimental investigations indicate that the cis azobenzene molecule commonly shows high conductance, while the trans azobenzene molecule shows low conductance. However, the computations give the opposite results. To reveal this significant difference, the effects of electrode mechanical modulation on the geometries and electronic transports of the azobenzene molecules are studied. The effects of the electrode geometries on the electronic transports of the azobenzene molecular junctions are also investigated. The electrode compressing process and the electrode stretching process of the azobenzene molecular junctions are simulated based on the first principles calculations. The electronic transport properties are further calculated by using non-equilibrium Green’s function (NEGF) method. The numerical results show that the structures of the cis and trans azobenzenes with sulfur anchors are stable in the stretching process and compressing process of electrode. For the cis azobenzene molecular junction, the cis geometry remains unchanged until the electrode distance is stretched to about 0.1 nm longer than the stable electrode distance of the trans azobenzene molecular junction. Though the trans azobenzene molecule is bent when squeezed by the electrodes, the C—N—N—C dihedral still maintains its trans structure even when the electrode distance is compressed to about 0.2 nm shorter than the stable electrode distance of the cis azobenzene molecular junctions. It is intriguing that the conductance values of cis and trans azobenzene molecular junctions vary inversely with the electrode distance. The conductance value of the cis azobenzene molecular junction increases with the elongating of the electrode distance, while the conductance value of the trans azobenzene molecular junction increases with the compression of the electrode. The conductance is very sensitive to the electrode distance for both the cis azobenzene molecular junction and the trans azobenzene molecular junctions, which can change more than 10 times with the change of the electrode distance. In the lower bias regime, the conductance of the trans azobenzene is higher than that of the cis one if the two electrodes are planar. However, when the molecule is sandwiched between two pyramid-shaped electrodes, the condutance of the cis azobenzene is higher. Thus, the higher conductance of cis azobenzene may be caused either by the pyramid-shaped electrodes or by the large electrode distance.