Due to the advantage of enhanced load-bearing capacity, the usage of pile–raft foundation systems for heavy structures is very common. In the present study, numerical modeling of pile–raft foundation systems having a single pile, 2 × 2, 3 × 3 pile groups subjected to vertical incremental loading, have been performed using commercially available three dimensional (3D) finite element (FEM) software-PLAXIS 3D. The properties of the multi-layer subsoil profile used in this numerical modeling are taken from the reported study. The validation of the model has been done with the results of the reported field test. The effects of various parameters like thickness of raft (tr), number of piles (N), diameter of pile (d), and length of piles (L/d) on the load-bearing capacity of pile–raft foundation system have been investigated considering the time effect. The load-sharing mechanism between raft and piles, variation of shear force and bending moment along the length of the piles are discussed in detail. The results of this numerical analysis help to understand the applicability of the pile–raft foundation for carrying heavy structural loads.