A deepwater breakwater is a sloping structure with water depth of 18～30 m and soft soil layers of more than 30 m thick. The foundation is partially excavated and replaced，and the original soft soils of more than 10m are retained in the foundation，resulting in a large settlement of the foundation. In order to accurately predict the foundation settlement after construction and reserve the settlement to meet the design requirements of the breakwater’s top elevation，we study the settlement deformation and stability of deep soft soil foundation of deepwater breakwater by numerical method. Under the prerequisite that the numerical model is verified trustworthy by a lot of measured data obtained from underwater foundation monitoring during construction ，we simulate the whole process of excavation，dump filling and long-term settlement of the breakwater，and obtain the final settlement，construction period settlement and post-construction settlement of each typical section，which could be used as reference for reserved post-construction settlement of the breakwater top and breakwater maintenance in the later period. Meanwhile，the model is also used to further check the safety and stability of the breakwater foundation.