Numerical simulation is an important method to study the structural vibration response. And artificial boundary conditions will directly affect the reliability of numerical simulation results. While when we conduct numerical simulation of vibration, it is often assumed the input surface to be a fixed boundary. The purpose of this paper is to make a study on rationality of this method by the use of simulation on a two-dimensional homogeneous elastic half-space model and a soil-structure dynamic interaction model. The results show that: when fixed boundary used, after the wave reflected to the fixed boundary, it couldn’t leave the calculation region and will reflects back into the calculation region again; when viscous boundary used, the energy will be absorbed by the bottom boundary when the wave achieved the viscous boundary. It simulates the real situation that the wave goes through boundary surface into the infinite medium. So, when carrying out numerical simulation on structural dynamic analysis, the selection of fixed boundary is inclined to an incorrect result, while the select of viscous boundary is more accurate and reasonable.