The dynamic response of two-phase saturated porous media is of great significance in the field of earthquake engineering. The solution to this problem is complicated due to the dynamic coupling between the solid and liquid phases. So, its volatility is very large using general numerical software, and the results are generally not ideal. Hence, it greatly hinders the speed of the numerical methods for the study of the two-phase coupling problem. In this paper, the advantages of COMSOL in solving the multi-field coupling problem is utilized, to provide the wave equation characteristics of the Biot-saturated porous medium u-U coupled mode, using a series of differential operators and matrix transformation. Then, the wave equation of the derivative is obtained, based on the generalized partial differential equation model in the COMSOL Multiphysics module to solve the converted wave equation, and the improved infinite element boundary is applied to the simulation of the infinite domain dynamic problem. To prove the scientific nature of this method, the following methods are used to verify the accuracy of the method. By comparing with the analytical solution of the dynamic response of a saturated porous medium, the feasibility and correctness of the proposed model is verified, and based on this method, the relationship between the screening efficiency of the open trenches in the saturated soil foundation and the Poisson's ratio and porosity of the saturated soil are discussed. Through the research and analysis in this paper, the solution to the numerical solution of the dynamic coupling equations of the saturated porous media is realized, and it can also provide some valuable reference for the design of the open trenches vibration isolation in the saturated soil foundation. On the other hand, it also provides some valuable reference for practical engineering applications.