The rapid development of high-speed transportation infrastructure such as highway and high-speed railway has resulted in the advancement of soft soil improvement techniques. Vacuum preloading combined with vertical drains has been proved to be an effective method in the treatment of soft foundation. A three-dimensional numerical analysis of the coupled methods was presented, in which the smear zone and the well resistance were taken into account. The variations of the basic soil parameters including the permeability coefficient and the coefficient of volume compressibility were considered in the numerical model. The result of the numerical model was then compared to the measured value. The results indicate that the decrease of coefficient of volume compressibility accelerates the consolidation of the soil while the influence of hydraulic conductivity is insignificant. A cube drain presents the closest result to the real situation compared to the other equivalent methods of prefabricated vertical drain (PVD). The case study indicates that the numerical model with variation of soil parameters is closer to the measured value than the numerical model without variation of soil parameters.