Based on the pile-soil soft support model, a simplified interaction finite element analysis model of soil- structure was established, and the nonlinear dynamic time history analysis was conducted for this model under different seismic excitations and different conditions of the pile-soil. The result shows that, under certain ground motion and soil-foundation conditions, the nonlinear effect of the upper structure can be greater than fixed base assumption, and pile-group-soil soft support model also influences the weak layer position on the upper structure. The analysis results and the existing test results are in good agreement. By using structural units to solve complex computational problems in geotechnical engineering, designers can carry out dynamic time history analysis and seismic evaluation for the superstructure quickly, accurately and efficiently.