Conductance of Si-2 cluster sandwiched between Au electrodes is investigated by the density functional theory combined with the non-equilibrium Green's function method. We simulate the Au-Si-2-Au junctions breaking process, calculate the corresponding cohesion energy in four different anchoring geometries, and obtain the equilibrium conductance and the projected density of states of junctions in optimal position, and find that all junctions have large conductance. In addition, we calculate the relationship of conductance with external bias voltage, and find that the conductance of hollow-hollow configuration is more stable than other three configurations when the applied bias voltage increases. The calculated results proved that the distance, coupling morphology of Si-2 cluster connected with electrodes and external bias voltage have an important effect on the conductance of nanoscale junctions. (C) 2013 Elsevier B. V. All rights reserved.