In order to solve the problem of uneven settlement and large deformation of thick marine soft clay foundation, this paper explores the feasibility of replacing the embankment fill of the expanded polystyrene with the background of Country Garden Road and Bridge in Johor Bahru, Malaysia. The numerical model of the expanded polystyrene embankment in the replacement zone is established. The basement stress, lateral soil pressure and settlement deformation of the subgrade before and after the replacement are analyzed. The optimal replacement thickness of the expanded polystyrene material is clarified. The applicability of the numerical model is verified by the results of the on-site monitoring of the expanded polystyrene embankment. The results show that the use of the expanded polystyrene to replace the embankment in the deep soft foundation of the sea can significantly reduce the overlying load on the subgrade, improve the uneven settlement of the subgrade and ensure the stability of the abutment and embankment. The optimal replacement thickness of the expanded polystyrene can be determined by the replacement effect with different thickness of the expanded polystyrene according to the economic applicability.