In this paper, the partitioned MPS-FEM method is employed for two-dimensional and three-dimensional free surface flow interacting with deformable structures. The discretization of fluid and structure govern equations relies independently on the Moving Particle Semi-implicit method (MPS) and Finite Element Method (FEM). Two types of interpolation techniques, including the Shape Function Based Interpolation Technique (SFBI) and Kernel Function Based Interpolation Technique (KFBI) are proposed on the fluid-structure isomerous interface. The performance of MPS-FEM coupled method is validated by a series of two-dimensional Fluid-Structure Interaction (FSI) tests, including precision test and convergence validation. The results obtained show good agreements with published experimental result as well as referenced numerical results. At last, an extension of aforementioned coupled method to three-dimensional model is performed to investigate characteristics of three-dimensional FSI phenomena. It indicates that partitioned MPS-FEM method is effective and stable for the simulation of free-surface flow interacting with deformable structures.