The mechanical properties of soil in soft soil area are poor, and the settlement of the underlying layer in the composite foundation accounts for a large proportion of the total settlement. At present, most of the research focuses on the settlement of the reinforced area, and the research on the settlement of the underlying layer is of great significance for the settlement of soft soil composite foundation. The differences in load transfer modes of soil and pile are analyzed, and based on the Boussinesq solution and Mindlin solution, a calculation method for the stress and settlement of the underlying layer in flexible and rigid pile composite foundation is proposed. The relative displacement of soil and pile in flexible pile composite foundation is small, and the negative friction can be ignored, but the influence of effective pile length should be considered. The relative displacement of soil and pile in rigid pile composite foundation is large, so the negative friction should be considered. Part of soil top stress is transmitted to the pile via negative friction, and then the pile axial force is transmitted back to the soil via positive friction. In addition to effective pile length, the change of stress transfer path caused by negative friction should also be considered in settlement calculation.