The nonlinear compressibility and permeability of soft soils is a key factor in the consolidation of both composite and natural foundations. However, there are few corresponding consolidation theories for vertical drain-stone column composite foundations in which the nonlinear consolidation characteristics of soils can be taken into account. In this study, a nonlinear consolidation model is established to describe the seepage relations between soft soils, vertical drains and stone columns. Then, a consolidation governing equation is derived, where the total excess pore water pressure (EPWP), u¯, is a variable, and the average consolidation degree defined by strain and stress of the composite foundation is obtained, respectively. Numerous calculations are performed to analyze the consolidation behaviors of such composite foundations. The results show that the installation of vertical drains can enhance the consolidation rate effectively; the external load and the initial modulus ratio of column to soil have an influence on the stress concentration effect of stone columns. Finally, the proposed analytical solution is applied to the settlement calculation for an actual project, and the calculated results are in good agreement with the measured data in the early and late stages of consolidation.