Many investigations indicate that molecular electronics opens up possibilities for continually miniaturizing the electronic devices beyond the limits of the standard silicon-based technologies. There have been significant experimental and theoretical efforts to build molecular junctions and to study their transport properties. The electron transport in molecular device shows clearly quantum effect, and the transport property for molecular device would be strongly affected by chemical and structural details, including the contact position and method between molecule and electrodes, the angle between two electrodes connecting to the molecule. Till now, the micro-fabrication technology still does not guarantee metal electrodes contacting the molecules surfaces ideally. During molecular device fabrication, any tiny variations for the contact configuration usually exist in the molecular device, which would change the device transport property. Hence, it is necessary to investigate the effects of electrode position and electrode cross section size on the transport property.We take Au-benzene-1, 4-dithiol (BDT)-Au (Au-BDT-Au) molecular junctions as example, and systematically calculate its transport properties with various contact positions, and several electrode cross section sizes. The contact face for Au electrode is set to be the (001) face. In the calculations, the density functional theory combined with the Keldysh non-equilibrium Green's function formalism is utilized. The local density approximation is selected as an exchange correlation potential, and atomic core is determined by the standard norm conserving nonlocal pseudo-potential.Our investigations show that the relative position between the electrodes plays a crucial role in the transport behavior of Au-BDT-Au device. When both electrodes are set to be at the counter-position, the preferable transport behavior could be found. The counter-position indicates that the two electrodes are on the same line, which is beneficial to the fabrication. As the angle, which is defined as the angle of electrode deviating from the axis, is larger than five degrees, the transport behavior deteriorates. Hence, the angle for the electrode deviating from its axis should be less than five degrees. To study the effect of electrode cross section size, we calculate the transport properties for three electrode cross sections, i.e. 3×4, 4×4 and 5×4 supercell. Our calculations indicate that when electrode cross section is less than 4×4, the transmission, near the Fermi level, is discontinuous, which would deteriorate the transport performance. Hence, the section size of electrode should not be less than 4×4. This research will provide a scientific index for the electrode position and its cross section size during the fabrication.