The inconstant well resistance effect, namely the changing discharge capacity of PVD with the foundation depth and consolidation time, is observed in drainage well under the vacuum preloading condition. Meanwhile, the partition of vertical drain zone and smear zone in 3D model is another challenging problem of finite element simulation. In order to simulate the actual conditions of vacuum preloading, a model with dimensionless parameters and considering well resistance in 3D finite element analysis is developed in this paper. An adaptive grid unit simplifies the drain zone and an equivalent method simplifies smear zone in simulation. The proposed procedure is applied to build the 3D finite element model of the reclamation project in Tianjin Port, and is verified by comparisons between the calculated data and the observed data.