To ensure the computational efficiency of large-scale models using finite element method(FEM) and the accuracy of their seismic response results, a seismic wave input formula adapted to the viscous-spring boundary is deduced according to the wave field separation theory, a method for extracting the control area of boundary nodes is given, and the program for automatic setting of viscous-spring boundary and seismic wave input is realized and verified after the secondary development of ABAQUS. On this basis, a two-dimensional soil model under the action of vertical incident shear wave(SV) is established to compare 12 different combinations of boundary conditions and seismic wave input methods. Based on the principle of transmission and reflection of seismic waves on discontinuous interfaces, the mechanism of interaction between viscous-spring boundary condition and several seismic wave input methods is revealed. The results illustrate that for the viscous-spring boundary, the calculation results using the equivalent nodal load input method are in good agreement with the theoretical solutions with a high calculation accuracy, while the energy absorption capacity of viscous-spring boundary is lost using the acceleration input or the displacement input methods. The research work can provide a reference for the accurate application of viscous-spring boundary and the reasonable selection of seismic wave input methods in seismic analysis of underground structures. © 2020, Science Press. All right reserved.