Foundation subsidence is an important factor affecting the life of the highway, as well as one of the important evaluation indicators of the foundation disposal measures. In this paper, by selecting typical foundations of Jile express highway, FLAC3D was used to simulate the natural foundation settlement under different subgrade height considering the impact of groundwater levels in the Yellow River flood area. The relationship between the time T (Month) from subgrade construction completed to stabilization and the subgrade height H was found as: T=0.36H2-1.63H+33.47, and the appropriate value of time was got to be placed under different circumstances.