Based on the three-dimensional Biot consolidation theory, the soft ground consolidation process under negative pressure was calculated with the three-dimensional finite element method by means of ABAQUS software, in which the modified Cam-clay model and the homogenization method of hydraulic conductivity were used and the smear effect was considered. The numerical results with different loading methods and varying hydraulic conductivity and depths of sealing were compared. It was found that the three-dimensional finite element method can reflect the consolidation process under negative pressure more accurately, and the calculated results with nodal loading in the sand cushion agree with the measured data. When the variation of hydraulic conductivity with the void ratio is considered, the results of surface settlement, settlement trend, and the degree of consolidation are closer to the actual conditions. The optimal effective depth of sealing is about 3 m.