The transport properties of a Si3 atomic wire system, which is formed by a Si3 cluster connected to two lithium electrodes with bias applied, is studied using the simulator Virtual NanoLab that is constructed based on the non-equilibrium Green’s function (NEGF) scheme. We investigated the Si3 atomic wire system under three strain conditions (tensile, compressive and shear). Different trends in the I-V characteristics are observed for the three cases at various applied biases. The transmission spectrum T(E, Vb), as a function of energy and applied biases, are analyzed. The interactions among eigenstates of the molecular projected self-consistent Hamiltonian (MPSH) strongly affect the transport properties of the system.