A model of consolidation for a single-drain well under vacuum preloading, based on Biot’s axisymmetric theory and considering the “real strain” hypothesis, was established using the finite element method. Degenerating the consolidation equation of real strain yielded the Barron’s classical free strain and equal strain equations. The free strain and equal strain finite element models were derived by imposing boundary and constraint conditions on the real strain FEM model. The validation of the simulation process confirmed that the numerical model achieved consistent outcomes, with the theoretical values postulating its effectiveness. The real strain model revealed the Mandel–Cryer effect of soil near the vertical drain during the initial vacuum preloading consolidation process, causing the effective stress to increase more than the effective stress generated by the vacuum pressure and leading to a greater reduction in the void ratio. This phenomenon is one of the reasons for clogging during the vacuum preloading process. However, the free strain and equal strain models cannot produce this effect because they cannot describe the coupling between soil deformation and fluid flow. The parameter analysis of the real strain model showed that as Poisson’s ratio for soil decreased, the consolidation rate of soil also decreased, while the Mandel–Cryer effect of soil increased.