In order to study the influence of flexible foundation on the stability of ICF facility due to ambient vibration, two models are established for the “rigid” foundation and the flexible foundation, respectively. The soil-structure interaction (SSI) is considered by setting the springs and dampers on the dummy boundary, and uncertain soil properties are simulated by setting some stochastic parameters for stiffness of the springs and damping factors of the dampers. The influences of SSI and uncertain soil properties on the response of ICF facility are revealed by comparing simulation results of the two models. The ratios of the major displacement response and the rotation response in the flexible foundation model to those in the “rigid” foundation model are 1.24 and 1.49, respectively.