Complex single/multi-body structures are generally found in ship and ocean engineering. They have the smooth, sharp, concave, and convex surface features in common. Precise modeling of the structures is the basis of numerical simulation. However, the most widely used explicit modeling method requires considerable manual operations. The result is also difficult to reproduce. Therefore, this paper presents a Radial basis function (RBF) based hierarchical (h-) adaptive Cartesian grid method. The RBF is introduced for arbitrary implicit modeling over the Cartesian framework. Thanks to its natural properties, the RBF is easy to use, highly automated, and only needs a set of scatter points for modeling. The block-based h-adaptive mesh refinement (AMR) combined with the RBF aims to enhance the local grid resolution. It accelerates the calculation of intersecting points compared with the uniform Cartesian grid. The accuracy, efficiency, and robustness of the proposed method are validated by the simulation of the 3D analytical ellipsoidal surface and the unclosed conic surface. To select suitable parameters, we thoroughly investigated the uncertainty factors including sample points, RBF functions, and h-AMR grids. The simulation results of the single/multi-body Wigley hull and KCS hull forms verified the proper selection of the factors and the feasibility of our method to solve practical problems.