Influence of contact geometry including coupling morphology and distances on electrical transport properties of Si₄ cluster coupled to two atomic Au(100)-3×3 electrodes is investigated from first principles with a combination of density functional theory and non-equilibrium Green's function method. Following situations of coupling morphology are considered:Si₄ cluster is sandwiched between two atomic Au electrodes at top to top, top to hollow, hollow to hollow position. We optimize geometry of junctions at different distances. We calculate cohesion energy and conductance of junctions as a function of distance d_z, and simulate Au-Si₄-Au junctions breaking process. We obtain equilibrium conductances of the most stable structures for different coupling morphology. They are 0.71 G₀, 0.96 G₀, 2.44 G₀, respectively. All junctions at stable structure have great conductance. In the range of voltage from -1.2 V to 1.2 V, I-V curve of junctions in the most stable structure shows linear characteristics. It shows that conductance is sensitive to coupling morphology and contact distance.