In this paper, the method of partitioned analysis of soil-structure interaction (PASSI) is used to simulate the raft foundation-concrete frame model and pile foundation-concrete frame model in the shaking table test of nuclear island plant on soft soil foundation. The RG160, Chi-Chi and Landers seismic waves with amplitude modulation of 0.05 g, 0.10 g and 0.20 g were chose as input to the two models. Under various working conditions, the soil and structure acceleration amplification coefficient, floor response spectrum, time history of soil pressure at the bottom of raft foundation, pile strain and pile bending moment of shaking table test and numerical simulation test are compared and analyzed. The results show that: the numerical simulation results can reflect the shaking table test results well. After the amplification of soil layer, with the increase of floor, the coefficient of acceleration amplification increases in shaking table test and numerical simulation test, reflecting the same pattern. The response spectrum of soil-structure system obtained by shaking table test and numerical simulation is related to the frequency spectrum characteristics of input ground motion and the vibration characteristics of the system. In the shaking table test, the raft foundation will be overturned, and the time history of soil pressure at the bottom of the raft foundation shows the phenomenon of‘high in the east and low in the west’. However, this phenomenon does not appear in the time history of soil pressure at the bottom of the raft foundation in the numerical simulation. The reason is that the contact nonlinearity between the soil and the foundation is not considered in the numerical simulation. The seismic response of the pile group in the numerical simulation is basically consistent with the macroscopic phenomenon of the test, and there is a quantitative difference, which may be caused by the nonlinearity of the pile in the numerical simulation.