Based on the construction process of soft-soil subgrade in a coastal area, a numerical model was established by using the finite element software Midas GTS. Based on the measured data of the project, the settlement laws of the phased filling process are analyzed in detail. The results show that during the phased filling of subgrade, the excess pore water pressure of the soil is changed by the filling loading, and the rate of consolidation of the soil is also reflected from another angle. With the increase of the phased filling height, the settlement of subgrade is increased also. Through software simulation of different filling heights, the settlement of the filling process is predicted. Based on this, the construction schedule can be adjusted to shorten the construction period.